Class: Small proteins

Usually dominated by metal ligand, heme, and/or disulfide bridges

Lineage:

1. Root: scop
2. Class: Small proteins
   Usually dominated by metal ligand, heme, and/or disulfide bridges

Folds:

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) (17)
   disulphide-bound fold; contains beta-hairpin with two adjacent disulphides
4. PMP inhibitors (1)
   disulphide-rich fold; all-beta: 3 antiparallel strands
5. Midkine (1)
   disulphide-rich fold; all-beta: 3 antiparallel strands
6. TSP-1 type 1 repeat (1)
   disulphide-rich fold; all-beta: 3 antiparallel strands
7. Amb V allergen (1)
   disulphide-rich; alpha+beta: 3 antiparallel strands followed by a short alpha helix
8. Snake toxin-like (1)
   disulphide-rich fold: nearly all-beta
9. BPTI-like (1)
   disulphide-rich alpha+beta fold
10. Defensin-like (1)
    Disulphide-rich fold, nearly all-beta
11. Hairpin loop containing domain-like (1)
    alpha+beta fold with two crossing loops
12. Neurotoxin III (ATX III) (1)
13. LDL receptor-like module (1)
14. Crambin-like (1)
    disulphide-rich alpha+beta fold
15. Kringle-like (1)
    disulphide-rich fold; nearly all-beta
16. Ovomucoid/PCI-1 like inhibitors (1)
    disulphide-rich small alpha+beta fold
17. Trefoil (1)
    disulphide-rich fold; duplication: consists of two homologous domains
18. Cystine-knot cytokines (1)
    disulphide-rich fold; common core is all-beta
19. Complement control module/SCR domain (1)
    disulphide-rich all-beta fold
20. Sea anemone toxin k (1)
    disulphide-rich all-alpha fold
21. Blood coagulation inhibitor (disintegrin) (1)
    small disulphide-rich
22. Methylamine dehydrogenase, L chain (1)
    disulphide-rich; nearly all-beta
23. Serine proterase inhibitors (1)
    disulphide-rich; nearly all-beta
24. TB module/8-cys domain (1)
    disulphide-rich; alpha+beta
25. TNF receptor-like (1)
    duplication: consists of three similar disulphide-rich domains
26. Heparin-binding domain from vascular endothelial growth factor (1)
    duplication: consists of two similar disulphide-rich domains, alpha+beta
27. Antifungal protein (AGAFP) (1)
    disulphide-rich; all-beta: open barrel, 5 strands; OB-fold-like
28. Fibronectin type I module (1)
    disulphide-rich, all-beta
29. Thyroglobulin type-1 domain (1)
    disulphide-rich, alpha+beta
30. Type X cellulose binding domain, CBDX (1)
    disulphide-rich, alpha+beta
31. Cellulose docking domain, dockering (1)
    disulphide-rich, alpha+beta
32. Carboxypeptidase inhibitor (1)
    disulphide-rich, alpha+beta
33. Serine proteinase inhibitor lekti, domain one (1)
    disulphide-rich, alpha+beta
34. Tachycitin (1)
    disulphide-rich
35. Pheromone ER-23 (1)
    disulphide-rich, all-alpha
36. Apical membrane antigen 1 (1)
    disulphide-rich, alpha+beta
37. GLA-domain (1)
    Calcium ion-bound
38. Cholecystokinin A receptor, N-domain (1)
    a few helical turns and a disulide-crosslinked loop
39. HIV-1 VPU cytoplasmic domain (1)
    a few helical turns assembled without a hydrophobic core?
40. HIPIP (high potential iron protein) (1)
    folds around 4Fe-4S cluster
41. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain (1)
    folds around 4Fe-4S cluster
42. C2H2 and C2HC zinc fingers (1)
    alpha+beta metal(zinc)-bound fold: beta-hairpin + alpha-helix
43. Zn2/Cys6 DNA-binding domain (1)
    all-alpha dimetal(zinc)-bound fold
44. Glucocorticoid receptor-like (DNA-binding domain) (1)
    alpha+beta metal(zinc)-bound fold
45. Retrovirus zinc finger-like domains (1)
    metal(zinc)-bound fold
46. Rubredoxin-like (10)
    metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2
47. Ribosomal protein L36 (1)
    zinc-bound beta-ribbon motif
48. Zinc-binding domain of translation initiation factor 2 beta (1)
    zinc-bound beta-ribbon motif
49. B-box zinc-binding domain (1)
    zinc-bound alpha+beta motif
50. RING finger domain, C3HC4 (1)
    dimetal(zinc)-bound alpha+beta motif; structurally diverse
51. Pyk2-associated protein beta ARF-GAP domain (1)
    zinc-bound alpha+beta motif
52. Metallothionein (1)
    metal(iron)-bound fold
    duplication: consists of clear structural/sequence repeats
53. Zinc domain conserved in yeast copper-regulated transcription factors (1)
    metal(zinc)-bound alpha+beta fold
54. Ada DNA repair protein, N-terminal domain (N-Ada 10) (1)
    metal(zinc)-bound alpha+beta fold
55. Cysteine-rich domain (1)
    dimetal(zinc)-bound alpha+beta fold
56. FYVE/PHD zinc finger (1)
    dimetal(zinc)-bound alpha+beta fold
57. Zn-binding domains of ADDBP (1)
    metal(zinc)-bound alpha+beta fold
58. Inhibitor of apoptosis (IAP) repeat (1)
    metal(zinc)-bound alpha+beta fold
59. TAZ domain (1)
    all-alpha fold; Zn-binding sites are in the loops connecting helices
60. Cysteine-rich DNA binding domain, (DM domain) (1)
    alpha-helical fold with two Zn-binding sites
61. Cysteine-rich domain of the chaperone protein DnaJ. (1)
    metal(zinc)-bound extended beta-hairpin fold