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. 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-like (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. Cellulose docking domain, dockering (1)
    disulphide-rich, alpha+beta
31. Carboxypeptidase inhibitor (1)
    disulphide-rich, alpha+beta
32. Tachycitin (1)
    disulphide-rich
33. GLA-domain (1)
    Calcium ion-bound
34. Cholecystokinin A receptor, N-domain (1)
    a few helical turns and a disulide-crosslinked loop
35. HIV-1 VPU cytoplasmic domain (1)
    a few helical turns assembled without a hydrophobic core?
36. HIPIP (high potential iron protein) (1)
    folds around 4Fe-4S cluster
37. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain (1)
    folds around 4Fe-4S cluster
38. C2H2 and C2HC zinc fingers (1)
    alpha+beta metal(zinc)-bound fold: beta-hairpin + alpha-helix
39. Zn2/Cys6 DNA-binding domain (1)
    all-alpha dimetal(zinc)-bound fold
40. Glucocorticoid receptor-like (DNA-binding domain) (1)
    alpha+beta metal(zinc)-bound fold
41. Retrovirus zinc finger-like domains (1)
    metal(zinc)-bound fold
42. Rubredoxin-like (9)
    metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2
43. Ribosomal protein L36 (1)
    zinc-bound beta-ribbon motif
44. B-box zinc-binding domain (1)
    zinc-bound alpha+beta motif
45. RING finger domain, C3HC4 (1)
    dimetal(zinc)-bound alpha+beta motif; structurally diverse
46. Pyk2-associated protein beta ARF-GAP domain (1)
    zinc-bound alpha+beta motif
47. Metallothionein (1)
    metal(iron)-bound fold
    duplication: consists of clear structural/sequence repeats
48. Zinc domain conserved in yeast copper-regulated transcription factors (1)
    metal(zinc)-bound alpha+beta fold
49. Ada DNA repair protein, N-terminal domain (N-Ada 10) (1)
    metal(zinc)-bound alpha+beta fold
50. Cysteine-rich domain (1)
    dimetal(zinc)-bound alpha+beta fold
51. FYVE/PHD zinc finger (1)
    dimetal(zinc)-bound alpha+beta fold
52. Zn-binding domains of ADDBP (1)
    metal(zinc)-bound alpha+beta fold
53. Inhibitor of apoptosis (IAP) repeat (1)
    metal(zinc)-bound alpha+beta fold
54. TAZ domain (1)
    all-alpha fold; Zn-binding sites are in the loops connecting helices
55. C-terminal domain of ProRS (1)
    metal(zinc)-bound alpha+beta fold
56. Cysteine-rich domain of the chaperone protein DnaJ. (1)
    metal(zinc)-bound extended beta-hairpin fold