Class: All alpha proteins

Lineage:

1. Root: scop
2. Class: All alpha proteins

Folds:

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