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. Type I dockerin domain (1)
   tandem repeat of two calcium-binding loop-helix motifs, distinct from the EF-hand
4. LEM/SAP HeH motif (4)
   helix-extended loop-helix; parallel helices
5. Cytochrome c (1)
   core: 3 helices; folded leaf, opened
6. DNA/RNA-binding 3-helical bundle (10)
   core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
7. RuvA C-terminal domain-like (6)
   3 helices; bundle, right-handed twist
8. Putative DNA-binding domain (1)
   core: 3 helices; architecture is similar to that of the "winged helix" fold but topology is different
9. Spectrin repeat-like (7)
   3 helices; bundle, closed, left-handed twist; up-and-down
10. Bacterial immunoglobulin/albumin-binding domains (1)
    3 helices; bundle, closed, left-handed twist; up-and-down
11. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (1)
    3 helices; bundle, closed, right-handed twist; up-and-down
12. Protozoan pheromone proteins (1)
    3 helices; bundle, closed, left-handed twist, up-and-down
13. Acyl-CoA binding protein-like (2)
    core: 3 helices; bundle, closed, left-handed twist; up-and-down
14. Kix domain of CBP (creb binding protein) (1)
    3 helices; bundle, partly opened
15. alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 (1)
    3 helices, the first one is shorter than the other two; bundle, partly opened
16. Thermostable subdomain from chicken villin headpiece (1)
    3 short helices; irregular array
17. TAF(II)230 TBP-binding fragment (1)
    3 short helices; irregular array
18. S15/NS1 RNA-binding domain (1)
    3 helices; irregular array
19. p8-MTCP1 (1)
    3 helices; irregular array; disulfide-rich
20. Frizzled cystein-rich domain (1)
    Core: 3 helices; irregular array; disulfide-rich
21. T4 endonuclease V (1)
    3 helices; irregular array
22. Fertilization protein (1)
    core: 3 helices; bundle, closed, right-handed twist; up-and-down
23. PGBD-like (1)
    core: 3 helices; bundle, closed, left-handed twist; parallel
24. HMG-box (1)
    3 helices; irregular array
25. Histone-fold (1)
    core: 3 helices; long middle helix is flanked at each end with shorter ones
26. Open three-helical up-and-down bundle (5)
    core: 3 helices; bundle, open
27. Four-helical up-and-down bundle (14)
    core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down
28. PTS-regulatory domain, PRD (1)
    core: 4 helices; bundle, closed, right-handed twist; 1 crossover connection
29. Ferritin-like (1)
    core: 4 helices; bundle, closed, left-handed twist; 1 crossover connection
30. 4-helical cytokines (1)
    core: 4 helices; bundle, closed; left-handed twist; 2 crossover connections
31. 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
32. Acyl carrier protein-like (3)
    4 helices, bundle; helix 3 is shorter than others; up-and-down
33. Bromodomain-like (4)
    4 helices; bundle; minor mirror variant of up-and-down topology
34. ROP-like (2)
    4 helices; dimer of identical alpha-hairpin subunits; bundle, closed, left-handed twist
35. Dimerization-anchoring domain of cAMP-dependent type II PK regulatory subunit (1)
    4 helices; bundle, closed, right-handed twist
36. Transcription factor IIA (TFIIA), N-terminal domain (1)
    4 helices; bundle, closed, right-handed twist
37. Ectatomin, A & B chains (1)
    4 helices; bundle, closed, left-handed twist
38. SinR repressor dimerisation domain-like (1)
    4 helices; bundle, closed, right-handed twist
39. lambda repressor-like DNA-binding domains (1)
    core: 4 helices; folded leaf, closed
40. Signal peptide-binding domain (1)
    4 helices; orthogonal array
41. Binding domain of Skn-1 (1)
    4 helices; the long C-terminal helix protrudes from the domain and binds to DNA
42. Helix-loop-helix DNA-binding domain (1)
    4-helices; bundle, closed, left-handed twist; 2 crossover connections
43. EF Hand-like (4)
    core: 4 helices; array of 2 hairpins, opened
44. Calponin-homology domain, CH-domain (1)
    core: 4 helices: bundle
45. Domain of poly(ADP-ribose) polymerase (1)
    core: 4 helices: bundle; unusual topology
46. MDM2 (1)
    core: 4 helices: open bundle; capped by two small 3-stranded beta-sheets
    duplication: consists of two structural repeats
47. Met repressor-like (1)
    core: 4 helices; array of 2 hairpins, opened
48. Disulphide-bond formation facilitator (DSBA), insertion domain (1)
    4 helices; bundle, partly opened, left-handed twist; up-and-down
49. Glutathione S-transferases, C-terminal domain (1)
    core: 4 helices; bundle, closed, left-handed twist; right-handed superhelix
50. Methionine synthase domain-like (2)
    4 helices; bundle, left-handed twist; right-handed superhelix
51. STAT-like (2)
    4 long helices; bundle, left-handed twist (coiled colil); right-handed superhelix
52. N-cbl like (3)
    4 helices; bundle, left-handed twist; left-handed superhelix
53. C-terminal domain of B transposition protein (1)
    4 helices; irregular array
54. RNA polymerase omega subunit (1)
    4 helices; irregular array
55. Anaphylotoxins (complement system) (1)
    4 helices; irregular array, disulphide-linked
56. Cytochrome c oxidase subunit h (1)
    4 helices; irregular array, disulphide-linked
57. Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin (1)
    4 helices; folded leaf; right-handed superhelix
58. p53 tetramerization domain (1)
    core: 4 helices; bundle
59. Bcr-Abl oncoprotein oligomerization domain (1)
    core: 4 long helices; bundle
60. Domain of early E2A DNA-binding protein, ADDBP (1)
    4 helices; bundle, partly opened
61. IHF-like DNA-binding proteins (1)
    core: 4 helices; bundle, partly opened, capped with a beta-sheet
62. CO dehydrogenase ISP C-domain like (1)
    core: 4 helices, bundle
63. Protein HNS-dependent expression A; HdeA (1)
    4 helices; the three last helices form a bundle similar to that of the RuvA C-domain
64. PABC (PABP) domain (1)
    4 helices; an orthogonal array
65. Chemotaxis receptor methyltransferase CheR, N-terminal domain (1)
    4 helices; an orthogonal array
66. PAH2 domain (1)
    4 helices; open up-and-down bundle; binds alpa-helical peptides
67. SAM domain-like (11)
    4-5 helices; bundle of two orthogonally packed alpha-hairpins; involved in the interactions with DNA and proteins
68. Retroviral matrix proteins (1)
    4-5 helices; right-handed superhelix
69. Hepatitis B viral capsid (hbcag) (1)
    5 helices; array; two long helices form a hairpin that dimerises into a 4-helical bundle
70. Apolipophorin-III (1)
    5 helices; bundle, closed, left-handed twist
71. Saposin-like (2)
    5 helices; folded leaf, closed
72. Annexin (1)
    5 helices; folded leaf, closed
73. Transducin (alpha subunit), insertion domain (1)
    5 helices; folded leaf
74. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain (1)
    5 helices; irregular array; left-handed superhelix
75. Left-handed superhelix (3)
    core: 4-5 helices; bundle; left-handed superhelix
76. N-terminal domain of the delta subunit of the F1F0-ATP synthase (1)
    core: 5 helices; bundle
77. Endoplasmic reticulum protein ERP29, C-domain (1)
    5 helices; bundle
78. Functional domain of the splicing factor Prp18 (1)
    core: 5 helices; bundle
79. Retrovirus capsid protein, N-terminal core domain (1)
    core: 5 helices; bundle
80. Cyclin-like (1)
    core: 5 helices; one helix is surrounded by the others
81. Arp2/3 complex 21 kDa subunit ARPC3 (1)
    5 helices; one helix is surrounded by the others
82. RNase III endonuclease domain (1)
    core: 5 helices; one helix is surrounded by the others
83. Ribosomal protein S7 (1)
    core: 5 helices; contains one more helix and a beta-hairpin outside the core
84. DNA polymerase III clamp loader subunits, C-terminal domain (1)
    core: 5 helices: bundle
85. Anti-sigma factor Asia (1)
    core: 5 helices: orthogonal array
86. Iron-dependent represor protein, dimerization domain (1)
    6 helices, homodimer of 3-helical domains
87. Glutamyl tRNA-reductase dimerization domain (1)
    6 helices, homodimer of 3-helical domains
88. DEATH domain (1)
    6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
89. Fatty acid responsive transcription factor FadR, C-terminal domain (1)
    core: 6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
90. Antitermination factor NusB (1)
    6 helices: bundle; one central helix is surrounded by 5 others
91. N-terminal domain of DnaB helicase (1)
    6 helices: array
92. FliG C-terminal domain (1)
    6 helices: array
93. Guanido kinases (1)
    irregular array of 6 short helices
94. Scaffolding protein gpD of bacteriophage procapsid (1)
    core: 6 helices; one central helix is surrounded by 5 others
95. Hemocyanin, N-terminal domain (1)
    6 helices; bundle; one central helix is surrounded by 5 others
96. Di-copper centre-containing domain (1)
    multihelical
97. DBL homology domain (1)
    multihelical; core: 5-helical bundle
98. LigA subunit of an aromatic-ring-opening dioxygenase LigAB (1)
    multihelical; contains compact array of 6 short helices
99. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain (1)
    multihelical bundle; contains buried central helix
100. Transcription factor STAT-4 N-domain (1)
     multihelical; can be divided into two subdomains
101. 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
102. Carbamoyl phosphate synthetase, large subunit connection domain (1)
     multihelical; consists of two all-alpha subdomains
     possible duplication: subdomains have similar topologies
103. Heme-dependent peroxidases (1)
     multihelical; consists of two all-alpha domains
104. Ribosomal protein L19 (L19e) (1)
     multihelical; consists of two different 3-helical domains connected by a long, partly helical linker
105. Influenza virus matrix protein M1 (1)
     multihelical; consists of two different all-alpha subdomains, 4 helices each
106. DNA-glycosylase (1)
     multihelical; consists of two all-alpha domains
107. Anticodon-binding (C-terminal) domain of glutamyl-tRNA synthetase (GluRS) (1)
     multihelical; consists of two all-alpha domains
108. 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
109. FAD-binding (C-terminal) domain of DNA photolyase (1)
     multihelical; consists of two all-alpha subdomains
110. 6-phosphogluconate dehydrogenase C-terminal domain-like (1)
     multihelical; common core is formed around two long antiparallel helices related by (pseudo) twofold rotation
111. Uteroglobin-like (1)
     multihelical
112. alpha/alpha toroid (4)
     multihelical; up to seven alpha-hairpins are arranged in closed circular array
113. Citrate synthase (1)
     multihelical; consists of two all-alpha domains
114. Cytochrome P450 (1)
     multihelical
115. FIS-like (1)
     multihelical; intertwined dimer of identical 4-helical subunits
116. Flagellar transcriptional activator FlhD (1)
     multihelical; forms intertwined dimer of identical 5-helical subunits
117. Trp repressor (1)
     multihelical; intertwined dimer of identical 6-helical subunits
118. Ribosomal protein L7/12, oligomerisation (N-terminal) domain (1)
     multihelical; intertwined tetramer
119. MHC class II-associated invariant chain ectoplasmic trimerization domain (1)
     multihelical; intertwined trimer of identical 3-helical subunits
120. Aldehyde ferredoxin oxidoreductase, C-terminal domains (1)
     multihelical; consists of two all-alpha domains
121. Acid phosphatase/Vanadium-dependent haloperoxidase (1)
     multihelical; core: 5-helical bundle; binds cofactor at the beginning of third helix
122. sigma70 subunit fragment from RNA polymerase (1)
     multihelical; consists of 3 all-alpha subdomains
123. DNA repair protein MutS, domain III (1)
     multihelical; consists of 2 all-alpha subdomains
124. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain (1)
     multihelical; bundle of longer and shorter helices
125. A virus capsid protein alpha-helical domain (1)
     multihelical; three-helical bundle in the core is surrounded by non-conserved helices
126. GTPase activation domain, GAP (1)
     multihelical
127. Ras GEF (1)
     multihelical
128. Telomeric repeat binding factor (TRF) dimerisation domain (1)
     multihelical; can be divided into an alpha-alpha superhelix domain and a long alpha-haipin dimerisation domain
129. alpha-alpha superhelix (13)
     multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
130. Lipoxigenase (1)
     multihelical
     large nearly all-alpha domain
131. gene 59 helicase assembly protein (1)
     multihelical; consists of two all-alpha subdomains
132. Tetracyclin repressor-like, C-terminal domain (1)
     multihelical; interlocked (homo)dimer
133. Skp1-Skp2 dimerisation domains (1)
     multihelical; interlocked heterodimer
134. Nuclear receptor ligand-binding domain (1)
     multihelical; 3 layers or orthogonally packed helices
135. Phospholipase C/P1 nuclease (1)
     multihelical
136. Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b (1)
     multihelical; can be divided into three subdomains
137. Serum albumin-like (1)
     multihelical; one domain consists of two similar disulphide-linked subdomains
138. L-aspartase-like (1)
     multihelical, consists of three all-alpha domains
139. Terpenoid synthases (1)
     multihelical; core: 8 helices (C-J) are arranged in 2 parallel layers
140. GroEL-like chaperones, ATPase domain (1)
     multihelical; 8 helices arranged in 2 parallel layers
141. Chorismate mutase II (1)
     multihelical; core: 6 helices, bundle
142. Peridinin-chlorophyll protein (1)
     multihelical: forms a boat-shaped protein shell around cofactors
143. Heme oxygenase (1)
     multihelical; bundle
144. Antioxidant defence protein AhpD (1)
     multihelical; bundle
145. Phospholipase A2, PLA2 (1)
     common core: 2 helices, disulphide-linked, and a calcium-binding loop
146. Fungal elicitin, plant patogen (1)
     5 helices: irregular disulfide-linked array; also contains a small b-hairpin
147. Tetraspanin (1)
     5 helices: irregular disulfide-linked array; form homodimer
148. Repressor of bacterial conjugation FinO (1)
     6 helices: irregular non-globular array; also contains two small b-hairpins
149. Nuclear receptor coactivator interlocking domain (1)
     3 helices, non-globular array; forms interlocked heterodimers with its targets
150. Non-globular all-alpha subunits of globular proteins (9)
151. Multiheme cytochromes (1)
     variable number of helices and little beta structure; not a true fold