Structural Classification of Proteins

Root: scop

Classes:

All alpha proteins (138)
1. Globin-like (2)
  core: 6 helices; folded leaf, partly opened
2. Long alpha-hairpin (11)
  2 helices; antiparallel hairpin, left-handed twist
3. Cytochrome c (1)
  core: 3 helices; folded leaf, opened
4. DNA/RNA-binding 3-helical bundle (11)
  core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
5. RuvA C-terminal domain-like (6)
  3 helices; bundle, right-handed twist
6. Putative DNA-binding domain (1)
  core: 3 helices; architecture is similar to that of the "winged helix" fold but topology is different
7. Spectrin repeat-like (6)
  3 helices; bundle, closed, left-handed twist; up-and-down
8. Bacterial immunoglobulin/albumin-binding domains (1)
  3 helices; bundle, closed, left-handed twist; up-and-down
9. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (1)
  3 helices; bundle, closed, right-handed twist; up-and-down
10. Protozoan pheromone proteins (1)
  3 helices; bundle, closed, left-handed twist, up-and-down
11. Acyl-CoA binding protein-like (2)
  core: 3 helices; bundle, closed, left-handed twist; up-and-down
12. Kix domain of CBP (creb binding protein) (1)
  3 helices; bundle, partly opened
13. alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 (1)
  3 helices, the first one is shorter than the other two; bundle, partly opened
14. Thermostable subdomain from chicken villin headpiece (1)
  3 short helices; irregular array
15. TAF(II)230 TBP-binding fragment (1)
  3 short helices; irregular array
16. S15/NS1 RNA-binding domain (1)
  3 helices; irregular array
17. p8-MTCP1 (1)
  3 helices; irregular array
18. T4 endonuclease V (1)
  3 helices; irregular array
19. Fertilization protein (1)
  core: 3 helices; bundle, closed, right-handed twist; up-and-down
20. Zn2+ DD-carboxypeptidase, N-terminal domain (1)
  core: 3 helices; bundle, closed, left-handed twist; parallel
21. HMG-box (1)
  3 helices; irregular array
22. Histone-fold (1)
  core: 3 helices; long middle helix is flanked at each end with shorter ones
23. Open three-helical up-and-down bundle (4)
  core: 3 helices; bundle, open
24. Four-helical up-and-down bundle (11)
  core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down
25. Ferritin-like (1)
  core: 4 helices; bundle, closed, left-handed twist; 1 crossover connection
26. 4-helical cytokines (1)
  core: 4 helices; bundle, closed; left-handed twist; 2 crossover connections
27. Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (1)
  core: 4 helices; bundle; one loop crosses over one side of the bundle
28. Acyl carrier protein-like (3)
  4 helices, bundle; helix 3 is shorter than others; up-and-down
29. Bromodomain-like (2)
  4 helices; bundle; minor mirror variant of up-and-down topology
30. ROP-like (2)
  4 helices; dimer of identical alpha-hairpin subunits; bundle, closed, left-handed twist
31. Dimerization-anchoring domain of cAMP-dependent type II PK regulatory subunit (1)
  4 helices; bundle, closed, right-handed twist
32. Transcription factor IIA (TFIIA), N-terminal domain (1)
  4 helices; bundle, closed, right-handed twist
33. Ectatomin, A & B chains (1)
  4 helices; bundle, closed, left-handed twist
34. SinR repressor dimerisation domain-like (1)
  4 helices; bundle, closed, right-handed twist
35. lambda repressor-like DNA-binding domains (1)
  core: 4 helices; folded leaf, closed
36. Signal peptide-binding domain (1)
  4 helices; orthogonal array
37. Binding domain of Skn-1 (1)
  4 helices; the long C-terminal helix protrudes from the domain and binds to DNA
38. Helix-loop-helix DNA-binding domain (1)
  4-helices; bundle, closed, left-handed twist; 2 crossover connections
39. EF Hand-like (3)
  core: 4 helices; array of 2 hairpins, opened
40. Calponin-homology domain, CH-domain (1)
  core: 4 helices: bundle
41. Domain of poly(ADP-ribose) polymerase (1)
  core: 4 helices: bundle; unusual topology
42. MDM2 (1)
  core: 4 helices: open bundle; capped by two small 3-stranded beta-sheets
  duplication: consists of two structural repeats
43. Met repressor-like (1)
  core: 4 helices; array of 2 hairpins, opened
44. Disulphide-bond formation facilitator (DSBA), insertion domain (1)
  4 helices; bundle, partly opened, left-handed twist; up-and-down
45. Glutathione S-transferases, C-terminal domain (1)
  core: 4 helices; bundle, closed, left-handed twist; right-handed superhelix
46. Methionine synthase domain-like (2)
  4 helices; bundle, left-handed twist; right-handed superhelix
47. STAT-like (2)
  4 long helices; bundle, left-handed twist (coiled colil); right-handed superhelix
48. N-cbl like (3)
  4 helices; bundle, left-handed twist; left-handed superhelix
49. C-terminal domain B transposition protein (1)
  4 helices; irregular array
50. Anaphylotoxins (complement system) (1)
  4 helices; irregular array, disulphide-linked
51. Cytochrome c oxidase subunit h (1)
  4 helices; irregular array, disulphide-linked
52. Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin (1)
  4 helices; folded leaf; right-handed superhelix
53. p53 tetramerization domain (1)
  core: 4 helices; bundle
54. Domain of early E2A DNA-binding protein, ADDBP (1)
  4 helices; bundle, partly opened
55. Prokaryotic DNA-bending protein (1)
  core: 4 helices; bundle, partly opened, capped with a beta-sheet
56. CO dehydrogenase ISP C-domain like (1)
  core: 4 helices, bundle
57. Protein HNS-dependent expression A; HdeA (1)
  4 helices; the three last helices form a bundle similar to that of the RuvA C-domain
58. Chemotaxis receptor methyltransferase CheR, N-terminal domain (1)
  4 helices; an orthogonal array
59. PAH2 domain (1)
  4 helices; open up-and-down bundle; binds alpa-helical peptides
60. SAM domain-like (10)
  4-5 helices; bundle of two orthogonally packed alpha-hairpins; involved in the interactions with DNA and proteins
61. Retroviral matrix proteins (1)
  4-5 helices; right-handed superhelix
62. Hepatitis B viral capsid (hbcag) (1)
  5 helices; array; two long helices form a hairpin that dimerises into a 4-helical bundle
63. Apolipophorin-III (1)
  5 helices; bundle, closed, left-handed twist
64. Saposin-like (2)
  5 helices; folded leaf, closed
65. Annexin (1)
  5 helices; folded leaf, closed
66. Transducin (alpha subunit), insertion domain (1)
  5 helices; folded leaf
67. Thermolysin-like metalloproteases, C-terminal domain (1)
  5 helices; bundle, closed
68. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain (1)
  5 helices; irregular array; left-handed superhelix
69. Left-handed superhelix (2)
  core: 4-5 helices; bundle; left-handed superhelix
70. N-terminal domain of the delta subunit of the F1F0-ATP synthase (1)
  core: 5 helices; bundle
71. Endoplasmic reticulum protein ERP29, C-domain (1)
  5 helices; bundle
72. Functional domain of the splicing factor Prp18 (1)
  core: 5 helices; bundle
73. Retrovirus capsid protein, N-terminal core domain (1)
  core: 5 helices; bundle
74. Cyclin-like (1)
  core: 5 helices; one helix is surrounded by the others
75. Ribosomal protein S7 (1)
  core: 5 helices; contains one more helix and a beta-hairpin outside the core
76. Iron-dependent represor protein, dimerization domain (1)
  6 helices, homodimer of 3-helical domains
77. DEATH domain (1)
  6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
78. Fatty acid responsive transcription factor FadR, C-terminal domain (1)
  core: 6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
79. Antitermination factor NusB (1)
  6 helices: bundle; one central helix is surrounded by 5 others
80. delta prime subunit of DNA polymerase III, C-domain (1)
  6 helices: bundle
81. N-terminal domain of DnaB helicase (1)
  6 helices: array
82. FliG C-terminal domain (1)
  6 helices: array
83. Guanido kinases (1)
  irregular array of 6 short helices
84. Scaffolding protein gpD of bacteriophage procapsid (1)
  core: 6 helices; one central helix is surrounded by 5 others
85. Hemocyanin, N-terminal domain (1)
  6 helices; bundle; one central helix is surrounded by 5 others
86. Di-copper centre-containing domain (1)
  multihelical
87. DBL homology domain (1)
  multihelical; core: 5-helical bundle
88. LigA subunit of an aromatic-ring-opening dioxygenase LigAB (1)
  multihelical; contains compact array of 6 short helices
89. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain (1)
  multihelical bundle; contains buried central helix
90. Transcription factor STAT-4 N-domain (1)
  multihelical; can be divided into two subdomains
91. Regulator of G-protein signalling, RGS (1)
  multihelical; consists of two all-alpha subdomains
  contains a 4-helical bundle with left-handed twist and up-and-down topology
92. Carbamoyl phosphate synthetase, large subunit connection domain (1)
  multihelical; consists of two all-alpha subdomains
  possible duplication: subdomains have similar topologies
93. Heme-dependent peroxidases (1)
  multihelical; consists of two all-alpha domains
94. Ribosomal protein L19 (L19e) (1)
  multihelical; consists of two different 3-helical domains connected by a long, partly helical linker
95. Influenza virus matrix protein M1 (1)
  multihelical; consists of two different all-alpha subdomains, 4 helices each
96. DNA-glycosylase (1)
  multihelical; consists of two all-alpha domains
97. Anticodon-binding (C-terminal) domain of glutamyl-tRNA synthetase (GluRS) (1)
  multihelical; consists of two all-alpha domains
98. R1 subunit of ribonucleotide reductase, N-terminal domain (1)
  multihelical consists of two all-alpha subdomains
  subdomain 1 (residues 10-100) is a 4-helical bundle
99. FAD-binding (C-terminal) domain of DNA photolyase (1)
  multihelical; consists of two all-alpha subdomains
100. 6-phosphogluconate dehydrogenase C-terminal domain-like (1)
  multihelical; common core is formed around two long antiparallel helices related by (pseudo) twofold rotation
101. Uteroglobin-like (1)
  multihelical
102. alpha/alpha toroid (4)
  multihelical; up to seven alpha-hairpins are arranged in closed circular array
103. Citrate synthase (1)
  multihelical; consists of two all-alpha domains
104. Cytochrome P450 (1)
  multihelical
105. FIS-like (1)
  multihelical; intertwined dimer of identical 4-helical subunits
106. Pleiotropic regulator of virulence genes, SarA (1)
  multihelical; forms intertwined dimer of identical 4-helical subunits
107. Trp repressor (1)
  multihelical; intertwined dimer of identical 6-helical subunits
108. Ribosomal protein L7/12, oligomerisation (N-terminal) domain (1)
  multihelical; intertwined tetramer
109. MHC class II-associated invariant chain ectoplasmic trimerization domain (1)
  multihelical; intertwined trimer of identical 3-helical subunits
110. Aldehyde ferredoxin oxidoreductase, C-terminal domains (1)
  multihelical; consists of two all-alpha domains
111. Acid phosphatase/Vanadium-dependent haloperoxidase (1)
  multihelical; core: 5-helical bundle; binds cofactor at the beginning of third helix
112. sigma70 subunit fragment from RNA polymerase (1)
  multihelical; consists of 3 all-alpha subdomains
113. DNA repair protein MutS, domain III (1)
  multihelical; consists of 2 all-alpha subdomains
114. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain (1)
  multihelical; bundle of longer and shorter helices
115. Bluetongue virus coat protein vp7 (BTV-10 vp7), alpha-helical domain (1)
  multihelical
116. GTPase activation domain, GAP (1)
  multihelical
117. Ras GEF (1)
  multihelical
118. alpha-alpha superhelix (11)
  multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
119. Lipoxigenase (1)
  multihelical
  large nearly all-alpha domain
120. gene 59 helicase assembly protein (1)
  multihelical; consists of two all-alpha subdomains
121. Tetracyclin repressor (Tet-repressor, TetR), C-terminal domain (1)
  multihelical; interlocked (homo)dimer
122. Skp1-Skp2 dimerisation domains (1)
  multihelical; interlocked heterodimer
123. Nuclear receptor ligand-binding domain (1)
  multihelical; 3 layers or orthogonally packed helices
124. Phospholipase C/P1 nuclease (1)
  multihelical
125. Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b (1)
  multihelical; can be divided into three subdomains
126. Serum albumin (1)
  multihelical; one domain consists of two similar disulphide-linked subdomains
127. L-aspartase-like (1)
  multihelical, consists of three all-alpha domains
128. Terpenoid synthases (1)
  multihelical; core: 8 helices (C-J) are arranged in 2 parallel layers
129. GroEL-like chaperones, ATPase domain (1)
  multihelical; 8 helices arranged in 2 parallel layers
130. Chorismate mutase II (1)
  multihelical; core: 6 helices, bundle
131. Peridinin-chlorophyll protein (1)
  multihelical: forms a boat-shaped protein shell around cofactors
132. Heme oxygenase-1 (HO-1) (1)
  multihelical; bundle
133. Phospholipase A2, PLA2 (1)
  common core: 2 helices, disulphide-linked, and a calcium-binding loop
134. Fungal elicitin, plant patogen (1)
  5 helices: irregular disulfide-linked array; also contains a small b-hairpin
135. Tetraspanin (1)
  5 helices: irregular disulfide-linked array; form homodimer
136. Repressor of bacterial conjugation FinO (1)
  6 helices: irregular non-globular array; also contains two small b-hairpins
137. Non-globular all-alpha subunits of globular proteins (8)
138. Multiheme cytochromes (1)
  variable number of helices and little beta structure; not a true fold
All beta proteins (93)
1. Immunoglobulin-like beta-sandwich (14)
  sandwich; 7 strands in 2 sheets; greek-key
  some members of the fold have additional strands
2. Common fold of diphtheria toxin/transcription factors/cytochrome f (7)
  sandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like fold
3. Prealbumin-like (6)
  sandwich; 7 strands in 2 sheets, greek-key
  variations: some members have additional 1-2 strands to common fold
4. HSP40/DnaJ peptide-binding domain (1)
  sandwich; 6-6 strands in 2 sheets
5. alpha-Amylase inhibitor tendamistat (1)
  sandwich; 6 strands in 2 sheets
6. Cupredoxins (1)
  sandwich; 7 strands in 2 sheets, greek-key
  variations: some memmbers have additional 1-2 strands
7. C2 domain-like (4)
  sandwich; 8 strands in 2 sheets; greek-key
8. TRAF domain (1)
  sandwich; 8 strands in 2 sheets; greek-key
9. Neurophysin II (1)
  sandwich; 8 strands in 2 sheets; meander
10. Viral coat and capsid proteins (1)
  sandwich; 8 strands in 2 sheets; jelly-roll
  variations: some members have additional 1-2 strands
11. gamma-Crystallin-like (1)
  sandwich; 8 strands in 2 sheets; greek-key
  duplication: has internal pseudo twofold symmetry
12. Lipase/lipooxygenase domain (1)
  sandwich; 8 strands in 2 sheets; complex topology
  duplication: has weak internal pseudo twofold symmetry
13. PNGase F-like (2)
  sandwich; 8 strands in 2 sheets; jelly-roll; duplication: consists of two domains of this fold that pack together in a similar assymetric fasion
14. Calpain large subunit, middle domain (domain III) (1)
  sandwich; 8 strands in 2 sheets; jelly-roll
15. HSP20-like chaperones (1)
  sandwich; 8 strands in 2 sheets; greek-key
16. Ecotin, trypsin inhibitor (1)
  sandwich; 8 strands in 2 sheets; complex topology with the crossing loops
17. Phosphatidylethanolamine binding protein (1)
  sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
18. Galactose-binding domain-like (1)
  sandwich; 9 strands in 2 sheets; jelly-roll
19. Segmented RNA-genome viruses' proteins (1)
  sandwich; 9 strands in 2 sheets; jelly-roll; form trimers
20. F-MuLV receptor-binding domain (1)
  sandwich; 9 strands in 2 sheets; greek-key; contains a few helices in loop regions
21. Adenovirus fiber protein head domain (knob domain) (1)
  sandwich, 10 strands in 2 sheets; greek-key
22. TNF-like (1)
  sandwich, 10 strands in 2 sheets; jelly-roll
23. Spermadhesin, CUB domain (1)
  sandwich, 10 strands in 2 sheets; jelly-roll
24. Hyaluronate lyase-like, C-terminal domain (1)
  sandwich, 10 strands in 2 sheets; "folded meander"
25. Osmotin, thaumatin-like protein (1)
  sandwich; 11 strands in 2 sheets
26. SMAD/FHA domain (1)
  sandwich; 11 strands in 2 sheets; greek-key
27. Soluble secreted chemokine inhibitor, VCCI (1)
  sandwich; 11 strands in 2 sheets; greek-key
28. Paculovirus p35 (1)
  sandwich; 14 strands in 2 sheets; greek-key
29. Concanavalin A-like lectins/glucanases (1)
  sandwich; 12-14 strands in 2 sheets; complex topology
30. Supersandwich (3)
  sandwich; 18 strands in 2 sheets
31. EV matrix protein (1)
  consists of two beta-sandwich domains of similar topologies
32. gp9 (1)
  consists of two different beta-sandwich domains unrelated to other beta-sandwich folds
33. ISP domain (1)
  consists of two all-beta subdomains: conserved small domain has a rubredoxin-like fold; larger domain consists of 6 beta-stands packed in either sandwich of two 3-stranded sheets or closed barrel (n=6; S=8)
34. SH3-like barrel (7)
  barrel, partly opened; n*=4, S*=8; meander
  the last strand is interrupted by a turn of 3-10 helix
35. GroES-like (2)
  contains barrel, partly opened; n*=4, S*=8; meander
36. PDZ domain-like (1)
  contains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix
37. N-terminal domains of the minor coat protein g3p (1)
  core: barrel, in some members open; n*=4, S*=8; meander
38. Sm motif of small nuclear ribonucleoproteins, SNRNP (1)
  core: barrel, open; n*=4, S*=8; meander; SH3-like topology
39. Ribosomal protein L14 (1)
  barrel, closed; n=5, S=8, meander
40. OB-fold (7)
  barrel, closed or partly opened n=5, S=10 or S=8; greek-key
41. Photosynthetic reaction centre, H-chain, cytoplasmic domain (1)
  core: barrel, partly opened; n*=5, S*=8; meander
42. beta-Trefoil (5)
  barrel, closed; n=6, S=12; and a hairpin triplet; meander
  duplication: has internal pseudo threefold symmetry
43. Reductase/isomerase/elongation factor common domain (3)
  barrel, closed; n=6, S=10; greek-key
44. EF-Tu/eEF-1alpha C-terminal domain (1)
  barrel, closed; n=6, S=10; greek-key
45. FMN-binding split barrel (1)
  barrel; n=6, S=10; greek-key
46. FMT C-terminal domain-like (1)
  barrel, open; n*=6, S*=10; greek-key
47. Trypsin-like serine proteases (1)
  barrel, closed; n=6, S=8; greek-key
  duplication: consists of two domains of the same fold
48. mu transposase, C-terminal domain (1)
  barrel; n=6, S=8, greek-key
49. Domain of alpha and beta subunits of F1 ATP synthase-like (2)
  barrel, closed; n=6, S=8; greek-key
50. Acid proteases (1)
  barrel, closed; n=6, S=10, complex topology
51. ValRS/IleRS editing domain (1)
  core: barrel, closed; n=6, S=8; topology is similar to that of the acid proteases barrel
52. Double psi beta-barrel (2)
  barrel, closed; n=6, S=10; complex topology with crossover (psi) loops
53. Ribosomal protein L25-like (1)
  barrel, closed; n=6, S=10; complex topology
54. Core binding factor beta (1)
  barrel, closed; n=6, S=10; meander; capped at both ends by alpha-helices
55. PH domain-like (1)
  barrel, partly opened; n*=6, S*=12; meander; capped by an alpha-helix
56. Transcription factor IIA (TFIIA), N-terminal domain (1)
  barrel, closed; n=6, S=12; mixed beta-sheet
57. Herpes virus serine proteinase, assemblin (1)
  core: barrel, closed; n=7, S=8; complex topology
58. Pyruvate kinase beta-barrel domain (1)
  barrel, closed; n=7, S=10; complex topology
59. XRCC4, N-terminal domain (1)
  barrel, closed; n=7, S=10; order: 1234765; strands 1 and 5 are parallel to each other
60. Lipocalins (1)
  barrel, closed or opened; n=8, S=12; meander
61. Streptavidin-like (3)
  barrel, closed; n=8, S=10; meander
62. Cyclophilin (peptidylprolyl isomerase) (1)
  barrel, closed; n=8, S=10; complex topology
63. Oncogene products (1)
  barrel, closed; n=8, S=10; one overside connection
64. Extracytoplasmic domain of cation-dependent mannose 6-phosphate receptor (1)
  barrel, partly open; n*=8, S*=10; one psi loop
65. tripple barrel (1)
  dimer of two non-identical subunits; forms two similar barrels, n=8, S=10 each, that are fused together with the formation of third barrel, n=6, S=8
66. 4-bladed beta-propeller (1)
  consists of four 4-stranded beta-sheet motifs; meander
67. 5-bladed beta-propeller (1)
  consists of five 4-stranded beta-sheet motifs; meander
68. 6-bladed beta-propeller (4)
  consists of six 4-stranded beta-sheet motifs; meander
69. 7-bladed beta-propeller (7)
  consists of seven 4-stranded beta-sheet motifs; meander
70. 8-bladed beta-propeller (2)
  consists of eight 4-stranded beta-sheet motifs; meander
71. alpha-Amylases, C-terminal beta-sheet domain (1)
  folded sheet; greek-key
72. WW domain-like (2)
  core: 3-stranded meander beta-sheet
73. Head domain of nucleotide exchange factor GrpE (1)
  small mixed beta-sheet, 4 "generalized" strands
74. Carbonic anhydrase (1)
  single sheet; 10 strands
75. Bacteriochlorophyl A protein (1)
  single sheet; 16 strands; meander
76. Outer surface protein A (1)
  single sheet; 21 strands; meander; the middle part is exposed on both sides
  duplication: contains beta-hairpin repeats
77. beta-Prism I (3)
  consists of 3 4-stranded sheets; strands are parallel to the 3-fold axis
  duplication: has internal pseudo threefold symmetry
78. beta-Prism II (1)
  consists of 3 4-stranded sheets; strands are perpendicular to the 3-fold axis
  duplication: consists of two domains of this fold
79. beta-Roll (1)
  contains a parallel beta-helix that binds calcium ions between its turns
80. Single-stranded right-handed beta-helix (2)
  superhelix with each turn made by 3 strands with short links
  duplication: turns of the helix are structural repeats
81. Single-stranded left-handed beta-helix (2)
  superhelix with each turn made by 3 strands with short links
82. Double-stranded beta-helix (5)
  one turn of helix is made by two pairs of antiparallel strands linked with short turns
  has appearance of a sandwich of distinct architecture and jelly-roll topology
83. Triple beta-spiral (1)
  trimer formed by the interlocking beta-hairpin repeat units
84. Barrel-sandwich hybrid (3)
  sandwich of half-barrel shaped beta-sheets
85. beta-clip (5)
  double-stranded ribbon sharply bent in two places; the ribbon ends form incomplete barrel; jelly-roll
86. Hedgehog/intein (Hint) domain (1)
  complex fold made of five beta-hairpin units and a b-ribbon arc
87. LexA/Signal peptidase (1)
  complex fold made of several coiled beta-sheets; contains an SH3-like barrel
88. RabGEF Mss4 (1)
  complex fold made of several coiled beta-sheets
89. Cyanovirin-N (1)
  complex fold made of two three stranded beta-sheets and two beta-hairpins
90. Head-binding domain of phage p22 tailspike protein (1)
  complex fold made of bifurcated and partly folded b-sheet
91. E2 regulatory, transactivation domain (1)
  complex fold made of bifurcated and coiled b-sheets
92. alpha-Subunit of urease, composite domain (1)
  pseudobarrel; mixed sheet of 7 strand folded upon itself and "buckled" by two beta-turns
93. Epsilon subunit of F1F0-ATP synthase N-terminal domain (1)
  pseudobarrel: sandwich of two sheets packed at a positive interstrand angle and interconnected with many short turns
Alpha and beta proteins (a/b) (97)
Mainly parallel beta sheets (beta-alpha-beta units)
1. TIM beta/alpha-barrel (23)
  contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
  the first six superfamilies have similar phosphate-binding sites
2. NAD(P)-binding Rossmann-fold domains (1)
  core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456
  The nucleotide-binding modes of this and the next two folds/superfamilies are similar
3. FAD/NAD(P)-binding domain (1)
  core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
4. Nucleotide-binding domain (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
5. N-terminal domain of MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase) (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group
6. Cellulases (1)
  variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567
7. PFL-like glycyl radical enzymes (1)
  contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel
8. The "swivelling" beta/beta/alpha domain (5)
  3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology
  this domain is thought to be mobile in all proteins known to contain it
9. Barstar-like (2)
  2 layers, a/b; parallel beta-sheet of 3 strands, order 123
10. Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (2)
  2 curved layers, a/b; parallel beta-sheet; order 1234...N
11. Outer arm dynein light chain 1 (1)
  (beta-beta-alpha)n superhelix
12. Ribosomal proteins L15p and L18e (1)
  core: three turns of irregular (beta-beta-alpha)n superhelix
13. SpoIIaa-like (2)
  core: 4 turns of a (beta-alpha)n superhelix
14. ClpP/crotonase (1)
  core: 4 turns of (beta-beta-alpha)n superhelix
15. BRCT domain (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
16. beta-subunit of the lumazine synthase/riboflavin synthase complex (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
17. Caspase-like (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
18. DNA glycosylase (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
19. Catalytic domain of malonyl-CoA ACP transacylase (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
20. Initiation factor IF2/eIF5b, domain 3 (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
21. Ribosomal protein L13 (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 3214
22. Ribosomal protein L4 (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 1423
23. Flavodoxin-like (16)
  3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
24. Methylglyoxal synthase-like (1)
  3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
25. Ferredoxin reductase-like, C-terminal NADP-linked domain (1)
  3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
26. Adenine nucleotide alpha hydrolase-like (3)
  core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
27. Pyrimidine nucleoside phosphorylase central domain (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
28. N-terminal domain of DNA photolyase (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
29. ETFP adenine nucleotide-binding domain-like (1)
  3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 32145
30. Biotin carboxylase N-terminal domain-like (1)
  3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strands
  possible rudiment form of Rossmann-fold domain
31. DHS-like NAD/FAD-binding domain (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-like
32. Tubulin, GTPase domain (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
33. Cysteine hydrolase (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
34. Halotolerance protein Hal3 (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
35. Glucosamine 6-phosphate deaminase/isomerase (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 324561
36. Thiamin diphosphate-binding fold (THDP-binding) (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
37. P-loop containing nucleotide triphosphate hydrolases (1)
  3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
38. Fructose permease, subunit IIb (1)
  3 layers: a/b/a, parallel beta-sheet of 6 strands, order 324156
39. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) (1)
  3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567
40. Methylesterase CheB, C-terminal domain (1)
  3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3421567
41. Subtilisin-like (1)
  3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3
42. Arginase/deacetylase (1)
  3 layers: a/b/a, parallel beta-sheet of 8 strands, order 21387456
43. CoA-dependent acyltransferases (1)
  core: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 are antiparallel to the rest
44. Phosphotyrosine protein phosphatases I-like (2)
  3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134
45. (Phosphotyrosine protein) phosphatases II (1)
  core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1432
46. Rhodanese/Cell cycle control phosphatase (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
47. Thioredoxin fold (3)
  core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest
48. Transketolase C-terminal domain-like (1)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 13245, strand 1 is antiparallel to the rest
49. Pyruvate kinase C-terminal domain-like (2)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallel to the rest
50. Leucine aminopeptidase, N-terminal domain (1)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 23145; strand 2 is antiparallel to the rest
51. Anticodon-binding domain-like (4)
  3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 4 is antiparallel to the rest
52. Restriction endonuclease-like (3)
  core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
53. Resolvase-like (2)
  Core: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
54. IIA domain of mannose transporter, IIA-Man (1)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
55. Ribonuclease H-like motif (7)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
56. Phosphorylase/hydrolase-like (6)
  core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
57. Molybdenumm cofactor biosynthesis protein MogA (1)
  3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallel to the rest; permutation of the Phosphorylase/hydrolase-like fold
58. Aminoacid dehydrogenase-like, N-terminal domain (1)
  3 layers: a/b/a; mixed beta-sheet of 5 strands; 12435, strand 2 is antiparallel to the rest
59. Glutamate ligase domain (1)
  3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 is antiparallel to the rest
60. Phosphoglycerate mutase-like (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 324156; strand 5 is antiparallel to the rest
61. PRTase-like (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
62. Integrin A (or I) domain (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
63. Glutaconate-CoA transferase subunits (1)
  core: 3 layers: a/b/a; parallel or mixed b-sheet of 6 strands, order 432156; part of sheet is folded upon itself and forms a barrel-like structure
64. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III (1)
  3 layers: a/b/a; mixed beta-sheet of 6 strands, order 231456; strand 3 is antiparallel to the rest
65. Formyltransferase (1)
  3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest
66. S-adenosyl-L-methionine-dependent methyltransferases (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
67. PLP-dependent transferases (1)
  main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest
68. Nucleotide-diphospho-sugar transferases (1)
  3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest
69. alpha/beta-Hydrolases (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 is antiparallel to the rest
70. Nucleoside hydrolase (1)
  core: 3 layers, a/b/a ; mixed beta-sheet of 8 strands, order 32145687; strand 7 is antiparallel to the rest
71. Dihydrofolate reductases (1)
  3 layers: a/b/a; mixed beta-sheet of 8 strands, order 34251687; strand 8 is antiparallel to the rest
72. Ribokinase-like (2)
  core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest
  potential superfamily: members of this fold have similar functions but different ATP-binding sites
73. Carbamate kinase-like (1)
  3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786; strand 8 is antiparallel to the rest
74. Class II aldolase (1)
  3 layers: a/b/a; mixed (mostly antiparallel) beta-sheet of 9 strands, order 432159876; left-handed crossover between strands 4 and 5
75. Cytosolic phospholipase A2 catalytic domain (1)
  3 layers: a/b/a; mixed beta-sheet of 9 strands, order 654321789; strands 4, 6 and 8 are antiparallel to the rest
76. Phosphatase/sulphatase (1)
  3 layers: a/b/a; mixed beta-sheet of 10 strands, order 564371892A, (A=10) strand 9 is antiparallel to the rest
77. Isocitrate & isopropylmalate dehydrogenases (1)
  consists of two intertwined (sub)domains related by pseudodyad; duplication
  3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest
78. ATC-like (2)
  consists of two similar domains related by pseudodyad; duplication
  core: 3 layers, a/b/a, parallel beta-sheet of 4 strands, order 2134
79. Tryptophan synthase beta subunit-like PLP-dependent enzymes (1)
  consists of two similar domains related by pseudodyad; duplication
  core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
80. SIS domain (1)
  consists of two similar domains related by pseudodyad; duplication
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345
81. Formate dehydrogenase/DMSO reductase, domains 1-3 (1)
  contains of two similar intertwined domains related by pseudodyad; duplication
  core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
82. Aldehyde reductase (dehydrogenase), ALDH (1)
  consists of two similar domains with 3 layers (a/b/a) each; duplication
  core: parallel beta-sheet of 5 strands, order 32145
83. Aconitase, first 3 domains (1)
  consists of three similar domains with 3 layers (a/b/a) each; duplication
  core: parallel beta-sheet of 5 strands, order 32145
84. Phosphoglucomutase, first 3 domains (1)
  consists of three similar domains with 3 layers (a/b/a) each; duplication
  core: mixed beta-sheet of 4 strands, order 2134, strand 4 is antiparallel to the rest
85. L-fucose isomerase, N-terminal and second domains (1)
  consists of two domains of similar topology, 3 layers (a/b/a) each
  Domain 1 (1-173) has parallel beta-sheet of 5 strands, order 21345
  Domain 2 (174-355) has parallel beta-sheet of 4 strands, order 2134
86. Phosphoglycerate kinase (1)
  consists of two non-similar domains, 3 layers (a/b/a) each
  Domain 1 has parallel beta-sheet of 6 strands, order 342156
  Domain 2 has parallel beta-sheet of 6 strands, order 321456
87. UDP-Glycosyltransferase/glycogen phosphorylase (1)
  consists of two non-similar domains with 3 layers (a/b/a) each
  domain 1: parallel beta-sheet of 7 strands, order 3214567
  domain 2: parallel beta-sheet of 6 strands, order 321456
88. Glutaminase/Asparaginase (1)
  consists of two non-similar alpha/beta domains, 3 layers (a/b/a) each
  Domain 1 has mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest; left-handed crossover connection between strands 4 and 5
  Domain 2 has parallel beta-sheet of 4 strands, order 1234
89. Phosphofructokinase (1)
  consists of two non-similar domains, 3 layers (a/b/a) each
  Domain 1 has mixed sheet of 7 strands, order 3214567; strands 3 & 7 are antiparallel to the rest
  Domain 2 has parallel sheet of 4 strands, order 2314
90. Cobalt precorrin-4 methyltransferase CbiF (1)
  consists of two non-similar domains
  Domain 1 has antiparallel sheet of 5 strands, order 32415
  Domain 2 has mixed sheet of 5 strands, order 12534; strands 4 & 5 are antiparallel to the rest
91. Phosphoenolpyruvate carboxykinase (ATP-oxaloacetate carboxy-liase) (1)
  consists of two alpa/beta domains
  duplication: the domains share an unusual fold of 2 helices and 6-stranded mixed sheet; beta(2)-alpha-beta(4)-alpha; order 312465, strands 1 and 5 are antiparallel to the rest
92. Chelatase-like (2)
  duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134
93. Periplasmic binding protein-like I (1)
  consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
  parallel beta-sheet of 6 strands, order 213456
94. Periplasmic binding protein-like II (1)
  consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
  mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
95. Thiolase-like (1)
  consists of two similar domains related by pseudodyad; duplication
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32451; strands 1 & 5 are antiparallel to the rest
96. Fe-only hydrogenase (1)
  consist of two intertwined domains; contains partial duplication
97. Cytidine deaminase (1)
  consists of two very similar domains with 3 layers (a/b/a)each; duplication
  mixed beta-sheet of 4 strands, order 2134; strand 2 is antiparallel to the rest
Alpha and beta proteins (a+b) (184)
Mainly antiparallel beta sheets (segregated alpha and beta regions)
1. Microbial ribonucleases (1)
  single helix packs against antiparallel beta-sheet
2. Lysozyme-like (1)
  common alpha+beta motif for the active site region
3. Cysteine proteinases (1)
  consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
4. His-Me finger endonucleases (1)
  core: (alpha)-beta-omega_loop-beta-alpha; embeded in larger different structures
5. RNase A-like (1)
  contains long curved beta-sheet and 3 helices
6. Prion protein domain (1)
  beta-alpha-beta-alpha(2); antiparallel beta-ribbon
7. LysM domain (1)
  beta-alpha(2)-beta;
8. Urease, gamma-subunit (1)
  alpha(3)-beta(2); antiparallel hairpin
9. IL8-like (2)
  beta(3)-alpha
10. DNA-binding domain (1)
  beta(3)-alpha; 2 layers: alpha/beta
11. Penicillin-binding protein 2x (pbp-2x), c-terminal domain (1)
  alpha1-beta3; 2 layers: alpha/beta; order 132
12. Ribosomal proteins L23 and L15e (1)
  beta-(alpha)-beta-alpha-beta(2); 3 layers: alpha/beta/alpha; antiparallel beta-sheet: order 1243
13. HIT-like (1)
  alpha-beta3-alpha-beta2; 3 layers: alpha/beta/alpha
14. Ribosomal protein S5 domain 2-like (1)
  core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
15. beta-Grasp (ubiquitin-like) (9)
  core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
16. FAD-linked reductases, C-terminal domain (1)
  alpha+beta sandwich
17. Cystatin-like (5)
  Core: alpha-beta(4); helix packs against coiled antiparallel beta-sheet
18. Transcriptional coactivator PC4 C-terminal domain (1)
  beta(4)-alpha; forms dimers by swapping helices
19. MHC antigen-recognition domain (1)
  dimeric
20. Ubiquitin conjugating enzyme (1)
  alpha-beta(4)-alpha(3); core: meander beta-sheet plus one helix 2
21. Diaminopimelate epimerase (1)
  mixed beta-sheet folds into a barrel (n=8, S=14) around the central helix
22. Fluorescent proteins (1)
  beta-sheet folds into a barrel (n=11, S=14) around the central helix
23. Transcriptional factor tubby, C-terminal domain (1)
  beta-sheet folds into a barrel (n=12, S=12) around the central helix
24. Pilin (1)
  contains very long N-terminal helix, which end is packed against beta-sheet
25. Acidic mitochondrial matrix protein p32 (1)
  core: beta(7)-alpha(2); N- and C-terminal extensions form a coiled coil subdomain
26. FKBP-like (3)
  core: beta(2)-alpha-beta(2); antiparallel beta-sheet
27. Ribosomal protein S16 (1)
  beta(4)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet, order: 51234
28. Ribosomal protein S19 (1)
  alpha-beta-X-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 123
29. Ribosomal protein L31e (1)
  beta-alpha-beta-(aplha)-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 1342
30. Allophycocyanin linker chain (domain) (1)
  beta(2)-alpha-beta; 2 layers: alpha/beta
31. Cdc48 domain 2-like (1)
  beta-alpha-beta(3); 2 layers: alpha/beta
32. Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (1)
  beta-alpha-beta(3); 2 layers: alpha/beta
33. Bacterial protein-export protein SecB (1)
  beta(4)-alpha(2); two layers: alpha/beta; antiparallel sheet: order 1432
34. DNA-binding domain of Mlu1-box binding protein MBP1 (1)
  beta(4)-alpha(2)-beta(2)-alpha; antiparallel sheet: order 123465
35. Heme-binding protein A (HasA) (1)
  beta-alpha-beta(6)-alpha(2); antiparallel sheet: order 165432
36. Chalcone isomerase (1)
  beta(3)-alpha(2)-beta-alpha(2)-beta3; 2 layers alpha/beta; antiparallel sheet: order 1234567
37. CBS-domain (1)
  core: beta-alpha-beta(4); 2 layers: alpha/beta
38. Thioesterase/thiol ester dehydrase-isomerase (1)
  core: beta-alpha-beta(4); 2 layers: alpha/beta
39. Dynein light chain 8 (DLC8) (1)
  core: beta-alpha(2)-beta-X-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 1342
40. CI-2 family of serine protease inhibitors (1)
  alpha+beta sandwich; loop across free side of beta-sheet
41. alpha/beta-Hammerhead (5)
  core: beta-BETA-alpha-beta-BETA-beta-alpha; contains a beta-hammerhead motif similar to that in barrel-sandwich hybrids
42. POZ domain (1)
  core: beta(2)-alpha(2)-beta(2)-alpha(2); 2 layers a/b; mixed sheet: 2143
43. Elongation factor Ts (EF-Ts), dimerisation domain (1)
  beta(2)-alpha(n)-beta; 2 layers a/b; antiparallel sheet: 123
44. Fe,Mn superoxide dismutase (SOD), C-terminal domain (1)
  alpha-beta(2)-alpha-beta-alpha(2); 3 strands of antiparallel sheet: 213
45. Ribosomal protein L7/12, C-terminal domain (1)
  beta-alpha(2)-beta-alpha-beta; 2 layers, alpha/beta
46. Transcription-state regulator AbrB, the N-terminal DNA recognition domain (1)
  beta-alpha-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123
47. Ribosomal protein L11, N-terminal domain (1)
  beta-alpha(2)-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123
48. Anti-LPS factor/recA domain (2)
  alpha-beta(3)-alpha(2); 2 layers, alpha/beta
49. Signal recognition particle alu RNA binding heterodimer, SRP9/14 (1)
  (beta)-alpha-beta(3)-alpha; 2 layers, alpha/beta
50. dsRBD-like (3)
  alpha-beta(3)-alpha; 2 layers: alpha/beta
51. KH-domain (1)
  beta-alpha(2)-beta(2)-alpha; 2 layers: alpha/beta
52. Alpha-lytic protease prodomain-like (3)
  core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta
53. Ribosomal protein S3 C-terminal domain (1)
  alpha(2)-beta(4); 2 layers: alpha/beta; antiparallel beta-sheet: order 2143
54. Enolase N-terminal domain-like (1)
  beta(3)-alpha(3); meander and up-and-down bundle
55. Ribosomal protein L22 (1)
  beta-alpha(3)-beta(2); 2 layers: alpha/beta; related to the enolase/MLE N-domain fold by a circular permutation
56. GroEL-like chaperone, intermediate domain (1)
  3-helical bundle packed against 3-stranded mixed beta-sheet
57. DNA damage-inducible protein DinI (1)
  beta-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed sheet 213; crossing loops
58. Ferredoxin-like (36)
  alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
59. Ribosomal protein L30p/L7e (1)
  core: beta-alpha-beta-alpha-beta; antiparallel beta-sheet: order 312; some similarity with the ferredoxin-like fold
60. Probable bacterial effector-binding domain (1)
  duplication of beta-alpha-beta(2) motif: antiparallel beta sheet forms barrel (n=6, S=12)
61. tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase (1)
  duplication of beta-alpha-beta-alpha-beta motif: antiparallel beta sheet forms barrel (n=6, S=8) similar to the barrel of prokaryotic DNA topoisomerases I and III
62. Pepsin inhibitor-3 (1)
  duplication of beta(3)-alpha(2) motif: meander beta sheets form barrel-like structure
63. mRNA triphosphatase CET1 (1)
  duplication of beta-alpha-beta(3) motif: antiparallel beta sheet forms wide barrel (n=8, S=16) with a channel running through it
64. eIF1-like (1)
  beta(2)-alpha-beta(2)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet: order 51243
65. Hedgehog/DD-pepidase (1)
  alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
66. Alpha-L RNA-binding motif (1)
  alpha(2)-beta(2)-loop-beta; 2 layers: alpha/beta
67. RRF/tRNA synthetase additional domain-like (3)
  core:alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
68. IF3-like (2)
  beta-alpha-beta-alpha-beta(2); 2 layers; mixed sheet 1243, strand 4 is antiparallel to the rest
69. C-terminal domain of TolA (1)
  alpha-beta(2)-alpha-beta; 2 layers, alpha/beta; left-handed beta-alpha-beta unit
70. Yest killer toxins (1)
  beta-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta; left-handed crossover connection
71. Cell division protein MinE topological specificity domain (1)
  dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
72. Cyanase C-terminal domain (1)
  intertwined dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
73. RuBisCO, small subunit (1)
  alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta
74. DCoH-like (4)
  beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
75. MutS N-terminal domain-like (2)
  beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
76. GYF domain (1)
  beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
77. Ribosomal protein L5 (1)
  beta-alpha-beta(2)-alpha-beta(3)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet: order 231654
78. RPB5-like RNA polymerase subunit (1)
  core: beta-alpha-beta-alpha-beta(2); 2 layers, alpha/beta
79. Bacillus chorismate mutase-like (4)
  core: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
80. Tautomerase/MIF (1)
  (beta-alpha-beta)2; 2 layers: alpha/beta; mixed beta-sheet
  forms trimers with three closely packed beta-sheets
81. Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (1)
  core: alpha-beta-alpha-beta(3); mixed sheet: 2134, strand 2 is parallel to strand 1
82. N domain of copper amine oxidase-like (2)
  alpha-beta(5)-alpha; 2 layers: alpha/beta; meander antiparallel sheet
83. Bactericidal permeability-increasing protein, BPI (1)
  beta-alpha-beta(5)-alpha-beta2; 2 layers: alpha/beta; antiparallel sheet
84. Subtilisin inhibitor (1)
  alpha+beta sandwich
85. RNA bacteriophage capsid protein (1)
  6-standed beta-sheet followed with 2 helices; meander
86. Translation initiation factor eIF4e (1)
  beta(2)-alpha-beta(2)-alpha-beta(2)-alpha-beta-2; 2 layers: alpha/beta; antiparallel sheet: 21356478
87. CO dehydrogenase flavoprotein C-domain-like (2)
  core: beta(3,4)-alpha(3); alpha+beta sandwich
88. SRF-like (1)
  alpha-beta(2)-alpha; dimer; 3 layers a/b/a; antiparallel beta-sheet
89. The origin DNA-binding domain of SV40 T-antigen (1)
  alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers:a/b/a; antiparallel sheet 41325
90. NADH oxidase/flavin reductase (1)
  core: (alpha-beta-alpha-beta)2; 3 layers a/b/a; antiparallel beta-sheet: 1243
91. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 (1)
  alpha-beta-alpha(2)-beta(3)-alpha; 3 layers a/b/a; antiparallel beta-sheet: 4123
92. Zincin-like (2)
  contains mixed beta sheet with connection over free side of the sheet
93. SH2-like (1)
  3 layers: a/b/a; antiparallel beta-sheet of 5 strands is flaked by two helices
94. Histidine-containing phosphocarrier proteins (HPr) (1)
  beta-alpha-beta(2)-alpha-beta-alpha; 2 layers: a/b; antiparallel sheet 1423
95. Homing endonuclease-like (2)
  alpha-beta(2)-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243
96. T-fold (1)
  beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1234
  tunnel-shaped: its known members form wide oligomeric barrels different sizes
97. Cell cycle regulatory proteins (1)
  beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1243
  can form strand-exchange dimers
98. beta-lactamase-inhibitor protein, BLIP (1)
  alpha(2)-beta(4); 2 layers: alpha/beta
99. Ribosomal protein L9 C-domain (1)
  alpha-beta-alpha(2)-beta(2); 2 layers: alpha/beta
100. L9 N-domain-like (1)
  beta(2)-alpha-beta-alpha; 3 layers: alpha/beta/alpha
101. Polynucleotide phosporylase/guanosine pentaphospate synthase (PNPase/GPSI), domains 2 and 5 (1)
  beta(2)-alpha-beta(2)-alpha; 3 layers: alpha/beta/alpha; antiparallel sheet: order 2134
102. Regulatory factor Nef (1)
  alpha(2)-beta(4)-alpha; 3 layers: alpha/beta/alpha
103. Mosquitocidal delta-endotoxin CytB (1)
  core: beta-alpha(2)-beta-alpha(2)-beta(4); 3 layers: a/b/a
104. Class II aaRS and biotin synthetases (1)
  contains large mixed beta-sheet
105. Clathrin adaptor appendage domain (1)
  beta-alpha-beta-alpha-beta(4)-alpha; 3 layers: a/b/a; bifurcated antiparallel beta-sheet
106. Sterol carrier protein 2 (SCP2) (1)
  alpha-beta(3)-(crossover)-beta-(alpha)-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 32145
107. Ran-binding protein mog1p (1)
  (beta-hairpin)-beta(3)-alpha-beta(4)-alpha; 3 layers: a/b/a; antiparallel beta-sheet of 7 strands; order: 1237654
108. Acyl-CoA N-acyltransferases (Nat) (1)
  3 layers: a/b/a; contains mixed beta-sheet
109. Actin depolymerizing proteins (1)
  3 layers: a/b/a; contains mixed beta-sheet
110. Profilin-like (3)
  core: 2 alpha-helices and 5-stranded sheet; 3 layers: alpha/beta/alpha
111. PR-1-like (1)
  alpha-beta-alpha-beta-alpha(2)-beta(2); 3 layers, alpha/beta/alpha; mixed sheet: order 1342
112. IIA domain of mannitol-specific and ntr phosphotransherase EII (1)
  beta-alpha(2)-beta(3)-alpha(3); 3 layers, alpha/beta/alpha; mixed sheet: order 1342
113. Nucleoside triphosphate pyrophosphorylase (MutT) (1)
  beta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet
  contains beta-grasp motif
114. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (1)
  core: alpha-beta(2)-alpha-beta(2)-alpha-beta; 3 layers; mixed sheet: order 31425
115. Hypothetica protein YrdC (1)
  core: alpha-beta(2)-alpha-beta-alpha(2)-beta(2)-alpha-beta-alpha-beta(3); 3 layers; mixed twisted sheet of 9 strands
116. Hypothetica protein HI1434 (YbaK homologue) (1)
  core: alpha-beta-alpha-beta(2)-(alpha-beta)2-alpha-beta(2)-alpha-beta; 3 layers; bifurcated mixed sheet
117. Thymidylate synthase/dCMP hydroxymethylase (1)
  contains large mixed beta-sheet
118. Bacteriophage T7 lysozyme (Zn amidase) (1)
  contains mixed beta-sheet
119. Streptomyces lysozyme (1)
  contains curved mixed beta-sheet; incomplete barrel
120. Cytochrome b5 (1)
  small, heme-binding fold
121. DNA topoisomerase I domain (1)
  beta(2)-alpha-beta-(alpha)-beta(2); left-handed crossover between strands 2 & 3
122. ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (1)
  8-stranded mixed beta-sheet; 2 layers: alpha/beta
123. Sporulation responce regulatory protein Spo0B (1)
  core: alpha-beta-alpha-beta(2)-(alpha)-beta(2)
124. Ribonuclease Rh-like (1)
  alpha+beta fold
125. Ornithine decarboxylase C-terminal domain (1)
  complex alpha+beta motif
126. Pentein, beta/alpha-propeller (1)
  duplication: composed of 5 alpha-beta(2)-alpha-beta units arranged around pseudo fivefold axis
127. Creatinase/aminopeptidase (1)
  duplication: composed of two very similar alpha+beta folds
128. Glutamine synthase/guanidino kinase catalytic domain (1)
129. TBP-like (3)
  beta-alpha-beta(4)-alpha
130. S-adenosylmethionine synthetase (1)
  duplication: consists of 3 similar intertwined domains
  structural repeat: beta-alpha-beta(2)-alpha-beta; two layers, alpha/beta
131. DNA clamp (1)
  contains two helices and two beta sheets
  duplication: fold has internal pseudo two-fold symmetry
132. Mitochondrial processing peptidase, MPP (1)
  beta(2)-alpha(2)-beta(2)-alpha(5)-beta; 2 layers: a/b; mixed sheet: order 15243: strands 2 to 5 are connected with a ferredoxin-like topology
133. Molybdemum cofactor-binding domain (1)
  beta(2)-alpha-beta-alpha-beta; 2 layers: a/b; mixed sheet: order 1243: crossing loops
134. Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 (1)
  beta-alpha-beta-alpha-beta(3)-alpha(2,3); mixed sheet: order 12345; left-handed crossover connection bettween strands 2 and 3
135. The spindle assembly checkpoint protein mad2 (1)
  beta-alpha(2)-beta(2)-alpha-beta(3); mixed sheet: order 132465
136. Phospholipase D/nuclease (1)
  beta-alpha-beta-alpha-beta-alpha-beta(4)-alpha; mixed sheet: order 1765234
137. Monooxygenase (hydroxylase) regulatory protein (1)
  corner-like structure formed by two sheets and filled in with 2-3 helices
138. B3/B4 domain of PheRS, PheT (1)
  3 layers: beta/beta/alpha sandwich
139. Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain (1)
  3 layers: alpha/beta/alpha; partial topological similarity to the ferredoxin-like fold
140. Ribosomal protein S8 (1)
  consists of 2 different alpha+beta subdomains arranged in a 4-layer structure: b/a/b/a
141. Ribosomal protein L6 (1)
  consists of two beta-sheets and one alpha-helix packed around single core
142. ATP-grasp (2)
  Consists of two subdomains with different alpha+beta folds
  shares functional and structural similarities with the PIPK and protein kinase superfamilies
143. SAICAR synthase-like (1)
  consists of two alpha+beta subdomains
144. Protein kinase-like (PK-like) (1)
  consists of two alpha+beta domains, C-terminal domain is mostly alpha helical
145. FAD-binding domain (1)
  consists of two alpha+beta subdomains
146. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain (1)
  consists of two alpha+beta subdomains
147. Methenyltetrahydromethanopterin cyclohydrolase (1)
  consists of two alpha+beta subdomains
148. Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap) (1)
  consists of two alpha+beta domains; the N-terminal domain is array of helices and beta-hairpins; the C-terminal domain is an a/b sandwich with one left-handed beta-alpha(n)-beta unit
149. Nitrile hydratase alpha chain (1)
  4 layers a/b/b/a; inside is a sandwich of two 2-stranded beta-sheets
150. 4'-Phosphopantetheinyl transferase SFP (1)
  4 layers a/b/b/a; duplication of beta-alpha(3)-beta(2) motif
151. DNase I-like (1)
  contains beta-sandwich; duplication of alpha+beta motif
152. Aldehyde ferredoxin oxidoreductase, N-terminal domain (1)
  contains sandwich; duplication of alpha+beta motif with single mixed sheet
  motif: beta(2)-alpha-beta(3)-alpha-beta; strand order 216345, strands 1 and 6 are parallel
153. N-terminal nucleophile aminohydrolases (Ntn hydrolases) (1)
  4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
154. L-aminopeptidase D-Ala-esterase/amidase (1)
  duplication of beta(3)-alpha-beta-alpha motif; 4 layers: alpha/beta/beta/alpha
155. Histidine decarboxylase (1)
  contains "silk" beta-sandwich flanked on both sides with alpha-helices
156. S-adenosylmethionine decarboxylase (1)
  duplication of beta-alpha-beta(4)-alpha-beta-alpha-beta(2) motif; 4 layers a/b/b/a; antiparallel beta-sheets: order 23451687
157. Metallo-hydrolase/oxidoreductase (1)
  duplication of beta(4)-alpha-beta-alpha motif; 4 layers a/b/b/a; mixed beta-sheets
158. Protein serine/threonine phosphatase 2C (1)
  4 layers: alpha/beta/beta/alpha; antiparallel beta sheets
159. Metallo-dependent phosphatases (1)
  4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
160. Nitrilase/N-carbamyl-D-aminoacid amidohydrolase (1)
  4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
161. Anthranilate synthase aminodeoxyisochorismate synthase/lyase subunit TrpE (1)
  duplication: contains four repeats of alpha-beta(2)-beta motif arranged in a 4 layer core structure: alpha/beta/beta/alpha; orthogonally packed beta-sheets
162. Lactate & malate dehydrogenases, C-terminal domain (1)
  unusual fold, defines family
163. DNA breaking-rejoining enzymes (1)
  core: alpha3-beta3-alpha4; one side of beta-sheet is exposed
164. SMAD MH1 domain (1)
  consists of four alpha-helices and three beta-ribbons
165. Ribosome inactivating proteins (RIP) (1)
  contains mixed beta-sheet
166. ADP-ribosylation (1)
  unusual fold
167. Peptide deformylase (1)
  alpha-beta(5)-alpha; 3 layers: a/b/a; meander beta-sheet wraps around the C-terminal alpha-helix
168. Succinate dehydrogenase/fumarate reductase catalytic domain (1)
  unusual fold
169. C-type lectin-like (1)
  unusual fold
170. SRCR-like (2)
  unusual fold; disulphide-rich; core: beta-x-alpha-beta-loop-beta
171. Fibrinogen C-terminal domains (1)
  unusual fold
172. gp120 core (1)
  unusual fold
173. Methionine synthase (activation domain) (1)
  unusual fold
174. Nitric oxide (NO) synthase oxygenase domain (1)
  unusual fold
175. Penicillin-binding protein 2x (pbp-2x), N-terminal domain (1)
  unusual fold
176. Sulfite oxidase, middle catalytic domain (1)
  unusual fold; contains 3 layers of beta-sheet structure and a beta-grasp like motif
177. Fumarylacetoacetate hydrolase, FAH (1)
  unusual fold; contains 3 layers of beta-sheet structure and a SH3-like like motif
178. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains (1)
  unusual fold
179. Substrate-binding domain of HMG-CoA reductase (1)
  unusual fold
180. Conserved core of transcriptional regulatory protein vp16 (1)
  unusual fold
181. Insert subdomain of RNA polymerase alpha subunit N-terminal domain (1)
  unusual fold; contains a left-handed beta-alpha-beta unit
182. Baseplate structural protein gp11 (1)
  unusual fold; trimer
183. Major capsid protein gp5 (1)
  unusual fold
184. Non-globular alpha_beta subunits of globular proteins (1)
Multi-domain proteins (alpha and beta) (28)
Folds consisting of two or more domains belonging to different classes
1. Serpins (1)
  contains a cluster of helices and a beta-sandwich
2. Replication terminator protein (Tus) (1)
  contains a cluster of helices and a beta-sandwich
3. beta-Lactamase/D-ala carboxypeptidase (1)
  contains a cluster of helices and an alpha+beta sandwich
4. ADP ribosyl cyclase (1)
  contains a cluster of helices and an alpha/beta domain
5. Heme-linked catalases (1)
  contains an (8,10) beta-barrel and an all-alpha domain
6. Acyl-CoA dehydrogenase (flavoprotein), N-terminal and middle domains (1)
7. Sugar phosphatases (1)
  N-terminal domain is an alpha+beta, C-terminal domain is an alpha/beta with mixed beta-sheet
8. DNA/RNA polymerases (1)
9. Nucleotidyltransferases (1)
  common catalytic domain is alpha+beta; 2 layers: a/b; mixed sheet
10. Prokaryotic type I DNA topoisomerase (1)
  4 domains: (1) Toprim alpha/beta; (2&4) "winged helix"-like; (3) barrel: n=6, S=8
11. Type II DNA topoisomerase (1)
  4 domains: (1) toprim alpha/beta; (2) "winged helix"-like; (3) alpha+beta; (4) all-alpha
12. DNA topoisomerase IV, alpha subunit (1)
  2 domains: (1) toprim alpha/beta; (2) "winged helix"-like
13. DNA primase DnaG catalytic core (1)
  3 domains: (1) toprim alpha+beta; (2) alpha/beta; (3) all-alpha
14. DNA repair protein MutM (Fpg) (1)
  3 domains: (1) beta-sandwich; (2) all-alpha (HhH-like motifs?; (3) zinc finger
15. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment (1)
  2 domains: alpha+beta and all-beta
16. DNA primase (1)
  3 domains: two alpha+beta domains and one all-alpha domain
17. D-amino acid aminotransferase-like PLP-dependent enzymes (1)
  2 domains: (1) alpha+beta: beta3-alpha2-beta2; (2) alpha/beta, a part of its mixed sheet forms barrel: n=6, S=8
18. Nickel-iron hydrogenase, large subunit (1)
  3 domains: (1) all-alpha; (2&3) alpha+beta
19. Nickel-iron hydrogenase, small subunit (1)
  2 domains: (1) alpa/beta; (2) Fe-S cluster-bound
20. Heat shock protein 70kD (HSP70), C-terminal, substrate-binding fragment (1)
  2 domains: (1) beta-sandwich: 8 strands in 2 sheets; (2) alpha-helical bundle
21. HAD-like (1)
  2 domains: (1) alpha/beta with a Rossmann-fold topology, (2) 4-helical bundle
22. Dehydroquinate synthase, DHQS (1)
  2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array
23. Firefly luciferase-like (1)
  4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta
24. Ribosomal protein L1 (1)
  2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
25. Neuronal Sec1, NSec1 (1)
  3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2
26. Hybrid cluster protein (prismane protein) (1)
  4 domains: (1 and 2) spectrin repeat-like 3-helical bundles; (3 and 4) alpha/beta: Rossmann-fold topology
27. Upper collar protein gp10 (connector protein) (1)
  2 domains: (1) alpha-helical bundle; (2) beta-barrel (n=5, S=8)
28. BTV inner layer core protein vp3 (1)
  large protein without apparent domain division; has a number of all-alpha regions and one all beta domain near the C-end
Membrane and cell surface proteins and peptides (11)
Does not include proteins in the immune system
1. Toxins' membrane translocation domains (5)
  multi-helical domains of various folds which is thought to unfold in the membrane
2. Membrane all-alpha (1)
3. Light-harvesting complex subunits (1)
  membrane all-alpha fold
4. Transmembrane beta-barrels (3)
  not a true fold, gathers together transmembrane barrels of different (n,S)
5. Integral outer membrane protein TolC, efflux pump component (1)
  subunit fold contains tandem repeat of alpha-beta hairpin-alpha(2) motif
  trimeric fold contains barrel (n=12, S=18) formed by beta-hairins, two from each subunit, and a bundle of helices with a channel running through it
6. Leukocidin (pore-forming toxin) (1)
  subunit fold contains beta-sandwich of Ig-like (grek-key) topology
  heptameric fold contains barrel (n=14, S=14) formed by beta-ribbon arms, one from each subunit
7. Lipovitellin-phosvitin complex (1)
8. (Pro)aerolysin, pore-forming lobe (1)
  3 domains: (1) alpha+beta; (2&3) all-beta
9. Perfringolysin (1)
  2 domains: (1) alpha+beta; (2) all-beta, similar to the CalB domain fold but the two last strands are transposed
10. Envelope glycoprotein, central and dimerisation domains (1)
  2 intertwined domains; all-beta and alpha+beta
11. Anthrax protective antigen (1)
  4 domains; I (res. 14-225) and II (226-487) are beta-sandwiches of similar gamma-crystallin like topologies; III (488-594) has a beta-grasp like fold; IV (595-735) has an Ig-like fold
Small proteins (54)
Usually dominated by metal ligand, heme, and/or disulfide bridges
1. Insulin-like (1)
  nearly all-alpha
  can be classified as disulphide-rich
2. Toxic hairpin (2)
  disulphide crosslinked alpha-helical hairpin
3. Knottins (small inhibitors, toxins, lectins) (16)
  disulphide-bound fold; contains beta-hairpin with two adjacent disulphides
4. Proteinase inhibitor PMP-C (1)
  disulphide-rich fold; all-beta: 3 antiparallel strands
5. Midkine (1)
  disulphide-rich fold; all-beta: 3 antiparallel strands
6. Amb V allergen (1)
  disulphide-rich; alpha+beta: 3 antiparallel strands followed by a short alpha helix
7. Snake toxin-like (1)
  disulphide-rich fold: nearly all-beta
8. BPTI-like (1)
  disulphide-rich alpha+beta fold
9. Defensin-like (1)
  Disulphide-rich fold, nearly all-beta
10. Hairpin loop containing domain of hepatocyte growth factor (1)
  alpha+beta fold with two crossing loops
11. Neurotoxin III (ATX III) (1)
12. Ligand-binding domain of low-density lipoprotein receptor (1)
13. Crambin-like (1)
  disulphide-rich alpha+beta fold
14. Kringle-like (1)
  disulphide-rich fold; nearly all-beta
15. Ovomucoid/PCI-1 like inhibitors (1)
  disulphide-rich small alpha+beta fold
16. Trefoil (1)
  disulphide-rich fold; duplication: consists of two homologous domains
17. Cystine-knot cytokines (1)
  disulphide-rich fold; common core is all-beta
18. Complement control module/SCR domain (1)
  disulphide-rich all-beta fold
19. Sea anemone toxin k (1)
  disulphide-rich all-alpha fold
20. Blood coagulation inhibitor (disintegrin) (1)
  small disulphide-rich
21. Methylamine dehydrogenase, L chain (1)
  disulphide-rich; nearly all-beta
22. Serine proterase inhibitors (1)
  disulphide-rich; nearly all-beta
23. TB module/8-cys domain (1)
  disulphide-rich; alpha+beta
24. TNF receptor-like (1)
  duplication: consists of three similar disulphide-rich domains
25. Heparin-binding domain from vascular endothelial growth factor (1)
  duplication: consists of two similar disulphide-rich domains, alpha+beta
26. Antifungal protein (AGAFP) (1)
  disulphide-rich; all-beta: open barrel, 5 strands; OB-fold-like
27. Fibronectin type I module (1)
  disulphide-rich, all-beta
28. Thyroglobulin type-1 domain (1)
  disulphide-rich, alpha+beta
29. Type X cellulose binding domain, CBDX (1)
  disulphide-rich, alpha+beta
30. Carboxypeptidase inhibitor (1)
  disulphide-rich, alpha+beta
31. Tachycitin (1)
  disulphide-rich
32. GLA-domain (1)
  Calcium ion-bound
33. Cholecystokinin A receptor, N-domain (1)
  a few helical turns and a disulide-crosslinked loop
34. HIV-1 VPU cytoplasmic domain (1)
  a few helical turns assembled without a hydrophobic core?
35. HIPIP (high potential iron protein) (1)
  folds around 4Fe-4S cluster
36. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain (1)
  folds around 4Fe-4S cluster
37. C2H2 and C2HC zinc fingers (1)
  alpha+beta metal(zinc)-bound fold: beta-hairpin + alpha-helix
38. Zn2/Cys6 DNA-binding domain (1)
  all-alpha dimetal(zinc)-bound fold
39. Glucocorticoid receptor-like (DNA-binding domain) (1)
  alpha+beta metal(zinc)-bound fold
40. Retrovirus zinc finger-like domains (1)
  metal(zinc)-bound fold
41. Rubredoxin-like (8)
  metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2
42. Ribosomal protein L36 (1)
  zinc-bound beta-ribbon motif
43. B-box zinc-binding domain (1)
  zinc-bound alpha+beta motif
44. RING finger domain, C3HC4 (1)
  dimetal(zinc)-bound alpha+beta motif; structurally diverse
45. Pyk2-associated protein beta ARF-GAP domain (1)
  zinc-bound alpha+beta motif
46. Metallothionein (1)
  metal(iron)-bound fold
  duplication: consists of clear structural/sequence repeats
47. Zinc domain conserved in yeast copper-regulated transcription factors (1)
  metal(zinc)-bound alpha+beta fold
48. Ada DNA repair protein, N-terminal domain (N-Ada 10) (1)
  metal(zinc)-bound alpha+beta fold
49. Cysteine-rich domain (1)
  dimetal(zinc)-bound alpha+beta fold
50. FYVE/PHD zinc finger (1)
  dimetal(zinc)-bound alpha+beta fold
51. Zn-binding domains of ADDBP (1)
  metal(zinc)-bound alpha+beta fold
52. Inhibitor of apoptosis (IAP) repeat (1)
  metal(zinc)-bound alpha+beta fold
53. TAZ domain (1)
  all-alpha fold; Zn-binding sites are in the loops connecting helices
54. Cysteine-rich domain of the chaperone protein DnaJ. (1)
  metal(zinc)-bound extended beta-hairpin fold
Coiled coil proteins (5)
1. Parallel coiled-coil (19)
  this is not a true fold; includes oligomers of shorter identical helices
2. Tetramerization domain of the Mnt repressor (1)
3. Stalk segment of viral fusion proteins (3)
  core: trimeric coiled coil
4. Antiparallel coiled-coil (6)
  this is not a true fold; contains at least two very long antiparallel helices
5. Apolipoprotein A-i (1)
  tetrameric antiparallel coiled coil, closed in a circuit
Low resolution protein structures (12)
1. Ribosome and ribosomal fragments (1)
2. Helicase (1)
3. ATP synthase (1)
4. Electron transport chains (1)
5. Photosystems (1)
6. Virus and virus-receptor complexes (1)
7. Reovirus core (1)
8. RNA polymerase (1)
9. Blood clotting (1)
10. Tubulin:stathmin-like domain complex (1)
11. Computational models partly based on NMR data (1)
12. Proteins of incorrect, partial and unknown sequence (1)
Peptides (77)
Peptides and fragments
1. Membrane ion channel-forming peptide antibiotics containing D-aminoacids (1)
2. Lantibiotic peptides (1)
  peptide antibiotic
3. Antimicrobial beta-hairpin (1)
  contains beta-hairpin crosslinked by disulphide bridge(s)
4. Antimicrobial helix (1)
  antibiotic peptide
5. Microcin J25 (1)
  mycrocyclic antimicrobial peptide; bacteriocin
6. Peptide hormones (1)
  contains one alpha-helix
7. delta-Toxin (1)
8. PSP1-like (1)
9. Arg-rich RNA binding peptides (6)
10. DNA-binding domains of HMG-I(Y) (1)
11. VPR protein fragments (1)
12. Inactivation gate of potassium and sodium channels (1)
13. Coagulation factor VIII, membrane-binding peptide (1)
14. Phosphocholine cytidylyltransferase membrane-binding peptides (1)
15. Parathyroid hormone fragments (residues between 1 and 39) (1)
16. Corticotropin releasing factor (1)
17. Liposaccharide-binding protein CAP18 (residues 106-137) (1)
18. Polymorphic antigen SPAM-H1 (residues 90-127) (1)
19. Mellitin (1)
20. Tertiapin (1)
  small disulphide-rich peptide
21. Antifreeze polypeptide HPLC-6 (1)
22. Troponin I fragments (1)
23. Pilin fragments (1)
24. RP71935 (1)
25. Atrial natriuretic peptide (1)
26. Compstatin (1)
27. Membrane-bound antimicrobial peptides (1)
28. Endothelin-like (1)
  small disulphide-rich
29. Heat-stable enterotoxin (HSE) (1)
30. Conotoxins (1)
  disulphide-rich fold
31. Conantokin (1)
32. Contryphan-R (1)
33. Immunodominant region of protein G of BRSV (1)
  hairpin of two short helices crosslinked with two disulphides
34. Bradykinin antagonist B-9340 (1)
35. Transmembrane helical fragments (1)
36. Topogenic peptides (3)
37. Phospholamban fragments (1)
38. Fragment of bowman-birk inhibitor (1)
39. Fragments of apolipoproteins (1)
40. Transactivation protein TAT (1)
41. Proline pipe (1)
42. Amyloid peptides (1)
43. Gelsolin fragment (residues 150-169) (1)
44. Acetylcholine receptor fragment (residues alpha 67-76) (1)
45. Thrombomodulin EGF domain fragment (residues 409-426) (1)
46. MoMLV p15 fragment (residues 409-426) (1)
47. Capsid protein major homology region peptide analog (1)
48. CD4 receptor peptide, res. 403-419 (1)
49. Heparin binding site of non collagenous domain I (nc1) of collagen facit xiv (1)
50. GroES, fragment of mobile loop (1)
51. cAMP and cGMP phosphodiesterase (PDE) fragments (1)
52. HIV-1 Nef protein fragments (1)
53. HIV-1 envelope gp120 protein concensus V3 loop peptide (1)
54. Hepatitis C virus N-terminal capsid protein fragment 2-45 (1)
55. P27(KIP1) fragment 22-106 (1)
56. Transducin alpha-1 subunit rhodopsin binding domain (res. 340-350) (1)
57. alpha-lactalbumin peptide model (1)
58. Coat protein-binding domain of bacteriophage p22 scaffolding protein (1)
59. Immunoreceptor tyrosine kinase activation motif, ITAM (1)
60. Cytoplasmic domain of the integrin alpha-iib subunit (1)
61. Human glutathione reductase (HGR) inhibitor (1)
62. Small subunit C-terminal inhibitory peptide of ribonucleotide reductase (1)
63. Histone H3 C-terminal fragment 130-135 (1)
64. Smad-binding domain of Sara (1)
65. Peptide derived from p-21 activated kinase (1)
66. pak1 autoregulatory domain (1)
67. Translocated intimin receptor (tir) intimin-binding domain (1)
68. Fragment 671-690 of the rabbit skeletal dihydropyridine receptor (1)
69. C-terminal negative regulatory domain of p53 (1)
70. FxFG nucleoporin repeats (1)
71. TCF3-CBD (catenin-binding domain) (1)
72. Synaptobrevin-II fragments (1)
73. VMIP-II fragment (1)
74. Papillomavirus e6-interacting peptide of e6ap (1)
75. Isolated insulin B-chain (1)
76. N-terminal hairpin of ubiquitin (residues 1-17) (1)
77. alpha-helical hairpin of p8mtcp1 (1)
Designed proteins (24)
Experimental structures of proteins with essentially non-natural sequences

Generated from scop database 1.55 with scopm 1.095 on Mon Jul 9 18:35:50 2001