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 (11)
   core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
7. Another 3-helical bundle (2)
   topologically similar to the DNA/RNA-binding bundles; distinct packing
8. RuvA C-terminal domain-like (5)
   3 helices; bundle, right-handed twist
9. S13-like H2TH domain (1)
   core: 3-4 helices
10. Putative DNA-binding domain (1)
    core: 3 helices; architecture is similar to that of the "winged helix" fold but topology is different
11. Spectrin repeat-like (7)
    3 helices; bundle, closed, left-handed twist; up-and-down
12. immunoglobulin/albumin-binding domain-like (2)
    3 helices; bundle, closed, left-handed twist; up-and-down; mirror topology to the spectrin-like fold
13. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (1)
    3 helices; bundle, closed, right-handed twist; up-and-down
14. Protozoan pheromone proteins (1)
    3 helices; bundle, closed, left-handed twist, up-and-down
15. Acyl-CoA binding protein-like (2)
    core: 3 helices; bundle, closed, left-handed twist; up-and-down
16. Kix domain of CBP (creb binding protein) (1)
    3 helices; bundle, partly opened
17. alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 (1)
    3 helices, the first one is shorter than the other two; bundle, partly opened
18. Thermostable subdomain from chicken villin headpiece (1)
    3 short helices; irregular array
19. TAF(II)230 TBP-binding fragment (1)
    3 short helices; irregular array
20. S15/NS1 RNA-binding domain (1)
    3 helices; irregular array
21. p8-MTCP1 (1)
    3 helices; irregular array; disulfide-rich
22. Frizzled cystein-rich domain (1)
    Core: 3 helices; irregular array; disulfide-rich
23. T4 endonuclease V (1)
    3 helices; irregular array
24. Fertilization protein (1)
    core: 3 helices; bundle, closed, right-handed twist; up-and-down
25. PGBD-like (1)
    core: 3 helices; bundle, closed, left-handed twist; parallel
26. HMG-box (1)
    3 helices; irregular array
27. Histone-fold (1)
    core: 3 helices; long middle helix is flanked at each end with shorter ones
28. Open three-helical up-and-down bundle (5)
    core: 3 helices; bundle, open
29. beta-catenin-interacting protein ICAT (1)
    core: 3 helices; irregular array
30. Four-helical up-and-down bundle (16)
    core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down
31. PTS-regulatory domain, PRD (1)
    core: 4 helices; bundle, closed, right-handed twist; 1 crossover connection
32. Ferritin-like (1)
    core: 4 helices; bundle, closed, left-handed twist; 1 crossover connection
33. 4-helical cytokines (1)
    core: 4 helices; bundle, closed; left-handed twist; 2 crossover connections
34. 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
35. Acyl carrier protein-like (3)
    4 helices, bundle; helix 3 is shorter than others; up-and-down
36. Bromodomain-like (4)
    4 helices; bundle; minor mirror variant of up-and-down topology
37. ROP-like (2)
    4 helices; dimer of identical alpha-hairpin subunits; bundle, closed, left-handed twist
38. Dimerization-anchoring domain of cAMP-dependent type II PK regulatory subunit (1)
    4 helices; bundle, closed, right-handed twist
39. Transcription factor IIA (TFIIA), N-terminal domain (1)
    4 helices; bundle, closed, right-handed twist
40. Ectatomin, A & B chains (1)
    4 helices; bundle, closed, left-handed twist
41. SinR repressor dimerisation domain-like (1)
    4 helices; bundle, closed, right-handed twist
42. lambda repressor-like DNA-binding domains (1)
    core: 4 helices; folded leaf, closed
43. Signal peptide-binding domain (1)
    4 helices; orthogonal array
44. A DNA-binding domain in eukaryotic transcription factors (1)
    4 helices; the long C-terminal helix protrudes from the domain and binds to DNA
45. Helix-loop-helix DNA-binding domain (1)
    4-helices; bundle, closed, left-handed twist; 2 crossover connections
46. EF Hand-like (4)
    core: 4 helices; array of 2 hairpins, opened
47. CH domain-like (2)
    core: 4 helices: bundle
48. Domain of poly(ADP-ribose) polymerase (1)
    core: 4 helices: bundle; unusual topology
49. MDM2 (1)
    core: 4 helices: open bundle; capped by two small 3-stranded beta-sheets
    duplication: consists of two structural repeats
50. Pre-protein croslinking domain of SecA (1)
    core: 4 helices: bundle; flanked by two short beta-hairpins
    duplication: consists of two structural repeats
51. Met repressor-like (1)
    core: 4 helices; array of 2 hairpins, opened
52. Disulphide-bond formation facilitator (DSBA), insertion domain (1)
    4 helices; bundle, partly opened, left-handed twist; up-and-down
53. Glutathione S-transferase (GST), C-terminal domain (1)
    core: 4 helices; bundle, closed, left-handed twist; right-handed superhelix
54. Methionine synthase domain-like (2)
    4 helices; bundle, left-handed twist; right-handed superhelix
55. STAT-like (2)
    4 long helices; bundle, left-handed twist (coiled colil); right-handed superhelix
56. N-cbl like (3)
    4 helices; bundle, left-handed twist; left-handed superhelix
57. C-terminal domain of B transposition protein (1)
    4 helices; irregular array
58. RNA polymerase omega subunit (1)
    4 helices; irregular array
59. Anaphylotoxins (complement system) (1)
    4 helices; irregular array, disulphide-linked
60. Cytochrome c oxidase subunit h (1)
    4 helices; irregular array, disulphide-linked
61. Crustacean CHH/MIH/GIH neurohormone (1)
    4 helices; irregular array, disulphide-linked
62. C-terminal domain of DFF45/ICAD (DFF-C domain) (1)
    4 helices; folded leaf; right-handed superhelix
63. Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin (1)
    4 helices; folded leaf; right-handed superhelix
64. p53 tetramerization domain (1)
    core: 4 helices; bundle
65. Bcr-Abl oncoprotein oligomerization domain (1)
    core: 4 long helices; bundle
66. Domain of early E2A DNA-binding protein, ADDBP (1)
    4 helices; bundle, partly opened
67. IHF-like DNA-binding proteins (1)
    core: 4 helices; bundle, partly opened, capped with a beta-sheet
68. CO dehydrogenase ISP C-domain like (1)
    core: 4 helices, bundle
69. Protein HNS-dependent expression A; HdeA (1)
    4 helices; the three last helices form a bundle similar to that of the RuvA C-domain
70. PABP domain-like (2)
    4 helices; an orthogonal array
71. Chemotaxis receptor methyltransferase CheR, N-terminal domain (1)
    4 helices; an orthogonal array
72. PAH2 domain (1)
    4 helices; open up-and-down bundle; binds alpa-helical peptides
73. Myosin phosphatase inhibitor 17kDa protein, CPI-17 (1)
    4 helices; open up-and-down bundle; the N-terminus is trapped within the bundle core
74. SAM domain-like (13)
    4-5 helices; bundle of two orthogonally packed alpha-hairpins; involved in the interactions with DNA and proteins
75. Retroviral matrix proteins (1)
    4-5 helices; right-handed superhelix
76. Hepatitis B viral capsid (hbcag) (1)
    5 helices; array; two long helices form a hairpin that dimerises into a 4-helical bundle
77. Apolipophorin-III (1)
    5 helices; bundle, closed, left-handed twist
78. Saposin-like (2)
    5 helices; folded leaf, closed
79. Annexin (1)
    5 helices; folded leaf, closed
80. Transducin (alpha subunit), insertion domain (1)
    5 helices; folded leaf
81. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain (1)
    5 helices; irregular array; left-handed superhelix
82. Left-handed superhelix (3)
    core: 4-5 helices; bundle; left-handed superhelix
83. N-terminal domain of the delta subunit of the F1F0-ATP synthase (1)
    core: 5 helices; bundle
84. ERP29 C domain-like (2)
    5 helices; bundle
85. Functional domain of the splicing factor Prp18 (1)
    core: 5 helices; bundle
86. Retrovirus capsid protein, N-terminal core domain (1)
    core: 5 helices; bundle
87. Cyclin-like (1)
    core: 5 helices; one helix is surrounded by the others
88. Arp2/3 complex 21 kDa subunit ARPC3 (1)
    5 helices; one helix is surrounded by the others
89. RNase III endonuclease catalytic domain (1)
    core: 5 helices; one helix is surrounded by the others
90. Ribosomal protein S7 (1)
    core: 5 helices; contains one more helix and a beta-hairpin outside the core
91. DNA polymerase III clamp loader subunits, C-terminal domain (1)
    core: 5 helices: bundle
92. Poly(A) polymerase, middle domain (1)
    core: 5-helical bundle; up-and-down; right-handed twist
93. Anti-sigma factor AsiA (1)
    core: 5 helices: orthogonal array
94. Iron-dependent represor protein, dimerization domain (1)
    6 helices, homodimer of 3-helical domains
95. Glutamyl tRNA-reductase dimerization domain (1)
    6 helices, homodimer of 3-helical domains
96. DEATH domain (1)
    6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
97. Fatty acid responsive transcription factor FadR, C-terminal domain (1)
    core: 6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
98. Antitermination factor NusB (1)
    6 helices: bundle; one central helix is surrounded by 5 others
99. N-terminal domain of DnaB helicase (1)
    6 helices: array
100. Guanido kinase N-terminal domain (1)
     irregular array of 6 short helices
101. Scaffolding protein gpD of bacteriophage procapsid (1)
     core: 6 helices; one central helix is surrounded by 5 others
102. Hemocyanin, N-terminal domain (1)
     6 helices; bundle; one central helix is surrounded by 5 others
103. Di-copper centre-containing domain (1)
     multihelical
104. DBL homology domain (DH-domain) (1)
     multihelical; core: 5-helical bundle
105. LigA subunit of an aromatic-ring-opening dioxygenase LigAB (1)
     multihelical; contains compact array of 6 short helices
106. RuBisCo LSMT C-terminal, substrate-binding domain (1)
     multihelical; irregular array of long and short helices
107. Porin chaperone SurA, peptide-binding domain (1)
     multihelical; irregular array of long and short helices
108. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain (1)
     multihelical bundle; contains buried central helix
109. Transcription factor STAT-4 N-domain (1)
     multihelical; can be divided into two subdomains
110. 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
111. GEF domain of SopE toxin (1)
     multihelical; consists of two all-alpha subdomains each containing a 3-helical bundle with right-handed twist
112. Variable surface antigen VlsE (1)
     multihelical; consists of two all-alpha subdomains; contains a 4-helical bundle with left-handed twist and up-and-down topology
113. Carbamoyl phosphate synthetase, large subunit connection domain (1)
     multihelical; consists of two all-alpha subdomains
     possible duplication: subdomains have similar topologies
114. Heme-dependent peroxidases (1)
     multihelical; consists of two all-alpha domains
115. Ribosomal protein L19 (L19e) (1)
     multihelical; consists of two different 3-helical domains connected by a long, partly helical linker
116. Influenza virus matrix protein M1 (1)
     multihelical; consists of two different all-alpha subdomains, 4 helices each
117. DNA-glycosylase (1)
     multihelical; consists of two all-alpha domains
118. An anticodon-binding domain of class I aminoacyl-tRNA synthetases (1)
     multihelical; consists of two all-alpha domains
119. 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
120. BEACH domain (1)
     multihelical, complex architecture
121. Cryptochrome/photolyase FAD-binding domain (1)
     multihelical; consists of two all-alpha subdomains
122. 6-phosphogluconate dehydrogenase C-terminal domain-like (1)
     multihelical; common core is formed around two long antiparallel helices related by (pseudo) twofold symmetry
123. Uteroglobin-like (1)
     multihelical
124. alpha/alpha toroid (5)
     multihelical; up to seven alpha-hairpins are arranged in closed circular array
125. Citrate synthase (1)
     multihelical; consists of two all-alpha domains
126. Cytochrome P450 (1)
     multihelical
127. FIS-like (1)
     multihelical; intertwined dimer of identical 4-helical subunits
128. Flagellar transcriptional activator FlhD (1)
     multihelical; forms intertwined dimer of identical 5-helical subunits
129. Ribosomal protein L7/12, oligomerisation (N-terminal) domain (1)
     multihelical; intertwined tetramer
130. MHC class II-associated invariant chain ectoplasmic trimerization domain (1)
     multihelical; intertwined trimer of identical 3-helical subunits
131. Aldehyde ferredoxin oxidoreductase, C-terminal domains (1)
     multihelical; consists of two all-alpha domains
132. Acid phosphatase/Vanadium-dependent haloperoxidase (1)
     multihelical; core: 5-helical bundle; binds cofactor at the beginning of third helix
133. BRCA2 helical domain (1)
     multihelical; contains a 3-helical bundle surrounded by several shorter helices
134. BRCA2 tower domain (1)
     multihelical; contains a 3-helical Hin recombinase-like subdomain and two long dimerisation helices
135. H-NS histone-like proteins (1)
     multihelical oligomeric protein; structure of whole subunit is not known yet but are probably composed of three different domains
136. RNA polymerase sigma subunit (1)
     multihelical; consists of several all-alpha subdomains
137. DNA repair protein MutS, domain III (1)
     multihelical; consists of 2 all-alpha subdomains
138. Helical scaffold and wing domains of SecA (1)
     multihelical; consists of 2 all-alpha subdomains
139. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain (1)
     multihelical; bundle of longer and shorter helices
140. A virus capsid protein alpha-helical domain (1)
     multihelical; three-helical bundle in the core is surrounded by non-conserved helices
141. GTPase activation domain, GAP (1)
     multihelical
142. Ras GEF (1)
     multihelical
143. 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
144. tRNA CCA-adding enzyme, C-terminal domains (1)
     multihelical; can be divided into three subdomains (neck, body and tail)
145. alpha-alpha superhelix (17)
     multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
146. Lipoxigenase (1)
     multihelical
     large nearly all-alpha domain
147. gene 59 helicase assembly protein (1)
     multihelical; consists of two all-alpha subdomains
148. Tetracyclin repressor-like, C-terminal domain (1)
     multihelical; interlocked (homo)dimer
149. Skp1 dimerisation domain-like (1)
     multihelical; interlocked heterodimer with F-box proteins
150. F-box domain (1)
     multihelical; interlocked heterodimer with the Skp1 dimerisation domain
151. Nuclear receptor ligand-binding domain (1)
     multihelical; 3 layers or orthogonally packed helices
152. Phospholipase C/P1 nuclease (1)
     multihelical
153. Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b (1)
     multihelical; can be divided into three subdomains
154. Serum albumin-like (1)
     multihelical; one domain consists of two similar disulphide-linked subdomains
155. L-aspartase-like (1)
     multihelical, consists of three all-alpha domains
156. Terpenoid synthases (1)
     multihelical; core: 8 helices (C-J) are arranged in 2 parallel layers
157. GroEL equatorial domain-like chaperone equatorial domain (1)
     multihelical; 8 helices arranged in 2 parallel layers
158. Chorismate mutase II (1)
     multihelical; core: 6 helices, bundle
159. Peridinin-chlorophyll protein (1)
     multihelical: forms a boat-shaped protein shell around cofactors
160. Heme oxygenase (1)
     multihelical; bundle
161. Antioxidant defence protein AhpD (1)
     multihelical; bundle
162. Double Clp-N motif (1)
     multihelical; array
163. Orange carotenoid protein, N-terminal domain (1)
     multihelical; array
164. N-terminal domain of bifunctional PutA protein (1)
     multihelical; array
165. Phospholipase A2, PLA2 (1)
     common core: 2 helices, disulphide-linked, and a calcium-binding loop
166. Fungal elicitin (1)
     5 helices: irregular disulfide-linked array; also contains a small beta-hairpin
167. Tetraspanin (1)
     5 helices: irregular disulfide-linked array; form homodimer
168. Repressor of bacterial conjugation FinO (1)
     6 helices: irregular non-globular array; also contains two small b-hairpins
169. Nuclear receptor coactivator interlocking domain (1)
     3 helices, non-globular array; forms interlocked heterodimers with its targets
170. Non-globular all-alpha subunits of globular proteins (9)
171. Multiheme cytochromes (1)
     variable number of helices and little beta structure; not a true fold