Class: Small proteins

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

Lineage:

1. Root: scop
2. Class: Small proteins [56992]
   Usually dominated by metal ligand, heme, and/or disulfide bridges

Folds:

1. Insulin-like [56993] (1)
   nearly all-alpha
   can be classified as disulfide-rich
2. Toxic hairpin [57006] (2)
   disulfide crosslinked alpha-helical hairpin
3. Knottins (small inhibitors, toxins, lectins) [57015] (19)
   disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
4. PMP inhibitors [57282] (1)
   disulfide-rich fold; all-beta: 3 antiparallel strands
5. Midkine [57287] (1)
   disulfide-rich fold; all-beta: 3 antiparallel strands
6. TSP-1 type 1 repeat [82894] (1)
   disulfide-rich fold; all-beta: 3 antiparallel strands
7. Amb V allergen [57295] (1)
   disulfide-rich; alpha+beta: 3 antiparallel strands followed by a short alpha helix
8. Snake toxin-like [57301] (1)
   disulfide-rich fold: nearly all-beta
9. BPTI-like [57361] (1)
   disulfide-rich alpha+beta fold
10. Defensin-like [57391] (1)
    Disulfide-rich fold, nearly all-beta
11. Hairpin loop containing domain-like [57413] (1)
    alpha+beta fold with two crossing loops
12. Neurotoxin III (ATX III) [57418] (1)
    disulfide-rich fold
13. LDL receptor-like module [57423] (1)
    disulfide-rich calcium-binding fold
14. Crambin-like [57428] (1)
    disulfide-rich alpha+beta fold
15. Kringle-like [57439] (1)
    disulfide-rich fold; nearly all-beta
16. Kazal-type serine protease inhibitors [100894] (1)
17. Plant proteinase inhibitors [100896] (1)
    disulfide-rich small alpha+beta fold; topological similarity to the Ovomucoid domain III
18. Trefoil/Plexin domain-like [57491] (2)
    disulfide-rich fold; common core is alpha+beta with two conserved disulfides
19. Necrosis inducing protein 1, NIP1 [103579] (1)
    disulfide-rich fold; all-beta; duplication: contains two structural repeats
20. Cystine-knot cytokines [57500] (1)
    disulfide-rich fold; common core is all-beta
21. Complement control module/SCR domain [57534] (1)
    disulfide-rich all-beta fold
22. Sea anemone toxin k [57545] (1)
    disulfide-rich all-alpha fold
23. Blood coagulation inhibitor (disintegrin) [57551] (1)
    small disulfide-rich
24. Methylamine dehydrogenase, L chain [57560] (1)
    disulfide-rich; nearly all-beta
25. Serine proterase inhibitors [57566] (1)
    disulfide-rich; nearly all-beta
26. TB module/8-cys domain [57580] (1)
    disulfide-rich; alpha+beta
27. TNF receptor-like [57585] (1)
    duplication: consists of three similar disulfide-rich domains
28. Heparin-binding domain from vascular endothelial growth factor [57592] (1)
    duplication: consists of two similar disulfide-rich domains, alpha+beta
29. Antifungal protein (AGAFP) [57597] (1)
    disulfide-rich; all-beta: open barrel, 5 strands; OB-fold-like
30. Fibronectin type I module [57602] (1)
    disulfide-rich, all-beta
31. Thyroglobulin type-1 domain [57609] (1)
    disulfide-rich, alpha+beta
32. Type X cellulose binding domain, CBDX [57614] (1)
    disulfide-rich, alpha+beta
33. Cellulose docking domain, dockering [64570] (1)
    disulfide-rich, alpha+beta
34. Carboxypeptidase inhibitor [57619] (1)
    disulfide-rich, alpha+beta
35. Invertebrate chitin-binding proteins [57624] (1)
    disulfide-rich
36. Pheromone ER-23 [69963] (1)
    disulfide-rich, all-alpha
37. Mollusk pheromone [90182] (1)
    disulfide-rich; all-alpha
38. Apical membrane antigen 1 [82909] (1)
    disulfide-rich, alpha+beta
39. Somatomedin B domain [90187] (1)
    disulfide-rich
40. Notch domain [90192] (1)
    disulfide-rich; all-alpha; calcium-binding
41. Mini-collagen I, C-terminal domain [103588] (1)
    disulfide-rich
42. GLA-domain [57629] (1)
    Calcium ion-bound
43. Cholecystokinin A receptor, N-domain [57641] (1)
    a few helical turns and a disulfide-crosslinked loop
44. HIV-1 VPU cytoplasmic domain [57646] (1)
    a few helical turns assembled without a hydrophobic core?
45. HIPIP (high potential iron protein) [57651] (1)
    folds around 4Fe-4S cluster
46. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57661] (1)
    folds around 4Fe-4S cluster
47. C2H2 and C2HC zinc fingers [57666] (1)
    alpha+beta metal(zinc)-bound fold: beta-hairpin + alpha-helix
48. Zn2/Cys6 DNA-binding domain [57700] (1)
    all-alpha dimetal(zinc)-bound fold
49. Glucocorticoid receptor-like (DNA-binding domain) [57715] (1)
    alpha+beta metal(zinc)-bound fold
50. SBT domain [103611] (1)
    consist of two different zn-binding subdomains, each subdomain resembles a distorted glucocorticoid receptor-like fold
51. Retrovirus zinc finger-like domains [57755] (1)
    metal(zinc)-bound fold
52. Rubredoxin-like [57769] (13)
    metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2
53. Ribosomal protein L36 [57839] (1)
    zinc-bound beta-ribbon motif
54. Zinc-binding domain of translation initiation factor 2 beta [75688] (1)
    zinc-bound beta-ribbon motif
55. B-box zinc-binding domain [57844] (1)
    zinc-bound alpha+beta motif
56. RING/U-box [57849] (1)
    dimetal(zinc)-bound alpha+beta motif; structurally diverse
57. Pyk2-associated protein beta ARF-GAP domain [57862] (1)
    zinc-bound alpha+beta motif
58. Metallothionein [57867] (1)
    metal(iron)-bound fold
    duplication: consists of clear structural/sequence repeats
59. Zinc domain conserved in yeast copper-regulated transcription factors [57878] (1)
    metal(zinc)-bound alpha+beta fold
60. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57883] (1)
    metal(zinc)-bound alpha+beta fold
61. Cysteine-rich domain [57888] (1)
    dimetal(zinc)-bound alpha+beta fold
62. FYVE/PHD zinc finger [57902] (1)
    dimetal(zinc)-bound alpha+beta fold
63. Zn-binding domains of ADDBP [57916] (1)
    metal(zinc)-bound alpha+beta fold
64. Inhibitor of apoptosis (IAP) repeat [57923] (1)
    metal(zinc)-bound alpha+beta fold
65. CCCH zinc finger [90228] (1)
    metal(zinc)-bound alpha+beta fold
66. Zinc finger domain of DNA polymerase-alpha [90233] (1)
    Zn-binding, all-alpha fold
67. TAZ domain [57932] (1)
    all-alpha fold; Zn-binding sites are in the loops connecting helices
68. Cysteine-rich DNA binding domain, (DM domain) [82926] (1)
    alpha-helical fold with two Zn-binding sites
69. DnaJ/Hsp40 cysteine-rich domain [57937] (1)
    metal(zinc)-bound extended beta-hairpin fold
70. CCHHC domain [103636] (1)
    metal(zinc)-bound fold
71. Sec-C motif [103641] (1)
    metal(zinc)-bound fold
72. TSP type-3 repeat [103646] (1)
    metal(calcium)-bound fold