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
   1. Insulin-like (1)
2. Toxic hairpin (2)
   disulphide crosslinked alpha-helical hairpin
   1. Heat-stable enterotoxin B (1)
   2. Neurotoxin B-IV (1)
3. Knottins (small inhibitors, toxins, lectins) (16)
   disulphide-bound fold; contains beta-hairpin with two adjacent disulphides
   1. Plant lectins/antimicrobial peptides (2)
   2. Plant inhibitors of proteinases and amylases (1)
   3. Cyclotides (3)
      macrocyclic plant knottins closed with the formation of an Asn-Gly peptide
   4. Gurmarin-like (2)
   5. Agouti-related protein (1)
   6. omega toxin-like (2)
   7. Scorpion toxin-like (5)
   8. Cellulose-binding domain (1)
   9. IGF binding domain (1)
   10. Colipase-like (1)
   11. EGF/Laminin (4)
   12. Bromelain inhibitor VI (cysteine protease inhibitor) (1)
   13. Bowman-Birk inhibitor, BBI (1)
   14. Elafin-like (1)
   15. Leech antihemostatic proteins (2)
   16. N-terminal domain of granulin-1 (1)
4. Proteinase inhibitor PMP-C (1)
   disulphide-rich fold; all-beta: 3 antiparallel strands
   1. Proteinase inhibitor PMP-C (1)
5. Midkine (1)
   disulphide-rich fold; all-beta: 3 antiparallel strands
   1. Midkine (2)
6. Amb V allergen (1)
   disulphide-rich; alpha+beta: 3 antiparallel strands followed by a short alpha helix
   1. Amb V allergen (1)
7. Snake toxin-like (1)
   disulphide-rich fold: nearly all-beta
   1. Snake toxin-like (3)
8. BPTI-like (1)
   disulphide-rich alpha+beta fold
   1. BPTI-like (2)
9. Defensin-like (1)
   Disulphide-rich fold, nearly all-beta
   1. Defensin-like (1)
10. Hairpin loop containing domain of hepatocyte growth factor (1)
    alpha+beta fold with two crossing loops
    1. Hairpin loop containing domain of hepatocyte growth factor (1)
       the middle part is structurally similar to some knottins and defensins but differs in the disulphide pattern
11. Neurotoxin III (ATX III) (1)
    1. Neurotoxin III (ATX III) (1)
12. Ligand-binding domain of low-density lipoprotein receptor (1)
    1. Ligand-binding domain of low-density lipoprotein receptor (1)
13. Crambin-like (1)
    disulphide-rich alpha+beta fold
    1. Crambin-like (1)
14. Kringle-like (1)
    disulphide-rich fold; nearly all-beta
    1. Kringle-like (2)
15. Ovomucoid/PCI-1 like inhibitors (1)
    disulphide-rich small alpha+beta fold
    1. Ovomucoid/PCI-1 like inhibitors (2)
       two families share the same beta-sheet topology but differ in the active-site loop location
16. Trefoil (1)
    disulphide-rich fold; duplication: consists of two homologous domains
    1. Trefoil (1)
17. Cystine-knot cytokines (1)
    disulphide-rich fold; common core is all-beta
    1. Cystine-knot cytokines (5)
18. Complement control module/SCR domain (1)
    disulphide-rich all-beta fold
    1. Complement control module/SCR domain (1)
19. Sea anemone toxin k (1)
    disulphide-rich all-alpha fold
    1. Sea anemone toxin k (1)
20. Blood coagulation inhibitor (disintegrin) (1)
    small disulphide-rich
    1. Blood coagulation inhibitor (disintegrin) (1)
21. Methylamine dehydrogenase, L chain (1)
    disulphide-rich; nearly all-beta
    1. Methylamine dehydrogenase, L chain (1)
22. Serine proterase inhibitors (1)
    disulphide-rich; nearly all-beta
    1. Serine proterase inhibitors (2)
23. TB module/8-cys domain (1)
    disulphide-rich; alpha+beta
    1. TB module/8-cys domain (1)
24. TNF receptor-like (1)
    duplication: consists of three similar disulphide-rich domains
    1. TNF receptor-like (1)
25. Heparin-binding domain from vascular endothelial growth factor (1)
    duplication: consists of two similar disulphide-rich domains, alpha+beta
    1. Heparin-binding domain from vascular endothelial growth factor (1)
26. Antifungal protein (AGAFP) (1)
    disulphide-rich; all-beta: open barrel, 5 strands; OB-fold-like
    1. Antifungal protein (AGAFP) (1)
27. Fibronectin type I module (1)
    disulphide-rich, all-beta
    1. Fibronectin type I module (1)
28. Thyroglobulin type-1 domain (1)
    disulphide-rich, alpha+beta
    1. Thyroglobulin type-1 domain (1)
29. Type X cellulose binding domain, CBDX (1)
    disulphide-rich, alpha+beta
    1. Type X cellulose binding domain, CBDX (1)
30. Carboxypeptidase inhibitor (1)
    disulphide-rich, alpha+beta
    1. Carboxypeptidase inhibitor (1)
31. Tachycitin (1)
    disulphide-rich
    1. Tachycitin (1)
32. GLA-domain (1)
    Calcium ion-bound
    1. GLA-domain (1)
       gamma-carboxy-glutamic acid-rich domain
33. Cholecystokinin A receptor, N-domain (1)
    a few helical turns and a disulide-crosslinked loop
    1. Cholecystokinin A receptor, N-domain (1)
34. HIV-1 VPU cytoplasmic domain (1)
    a few helical turns assembled without a hydrophobic core?
    1. HIV-1 VPU cytoplasmic domain (1)
35. HIPIP (high potential iron protein) (1)
    folds around 4Fe-4S cluster
    1. HIPIP (high potential iron protein) (1)
36. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain (1)
    folds around 4Fe-4S cluster
    1. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain (1)
37. C2H2 and C2HC zinc fingers (1)
    alpha+beta metal(zinc)-bound fold: beta-hairpin + alpha-helix
    1. C2H2 and C2HC zinc fingers (2)
38. Zn2/Cys6 DNA-binding domain (1)
    all-alpha dimetal(zinc)-bound fold
    1. Zn2/Cys6 DNA-binding domain (1)
       duplication: two structural repears are related by the pseudodyad
39. Glucocorticoid receptor-like (DNA-binding domain) (1)
    alpha+beta metal(zinc)-bound fold
    1. Glucocorticoid receptor-like (DNA-binding domain) (7)
40. Retrovirus zinc finger-like domains (1)
    metal(zinc)-bound fold
    1. Retrovirus zinc finger-like domains (1)
41. Rubredoxin-like (8)
    metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2
    1. Methionyl-tRNA synthetase (MetRS), Zn-domain (1)
    2. Microbial and mitochondrial ADK, insert "zinc finger" domain (1)
    3. Zinc beta-ribbon (3)
    4. Casein kinase II beta subunit (1)
    5. Rubredoxin-like (3)
    6. Hypothetical protein MTH1184 (1)
       contains two CXC motifs
    7. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain (1)
    8. Zn-binding ribosomal proteins (3)
42. Ribosomal protein L36 (1)
    zinc-bound beta-ribbon motif
    1. Ribosomal protein L36 (1)
43. B-box zinc-binding domain (1)
    zinc-bound alpha+beta motif
    1. B-box zinc-binding domain (1)
44. RING finger domain, C3HC4 (1)
    dimetal(zinc)-bound alpha+beta motif; structurally diverse
    1. RING finger domain, C3HC4 (1)
45. Pyk2-associated protein beta ARF-GAP domain (1)
    zinc-bound alpha+beta motif
    1. Pyk2-associated protein beta ARF-GAP domain (1)
46. Metallothionein (1)
    metal(iron)-bound fold
    duplication: consists of clear structural/sequence repeats
    1. Metallothionein (1)
47. Zinc domain conserved in yeast copper-regulated transcription factors (1)
    metal(zinc)-bound alpha+beta fold
    1. Zinc domain conserved in yeast copper-regulated transcription factors (1)
48. Ada DNA repair protein, N-terminal domain (N-Ada 10) (1)
    metal(zinc)-bound alpha+beta fold
    1. Ada DNA repair protein, N-terminal domain (N-Ada 10) (1)
49. Cysteine-rich domain (1)
    dimetal(zinc)-bound alpha+beta fold
    1. Cysteine-rich domain (2)
50. FYVE/PHD zinc finger (1)
    dimetal(zinc)-bound alpha+beta fold
    1. FYVE/PHD zinc finger (2)
51. Zn-binding domains of ADDBP (1)
    metal(zinc)-bound alpha+beta fold
    1. Zn-binding domains of ADDBP (1)
       duplication: contains two Zn-binding domains of similar fold
52. Inhibitor of apoptosis (IAP) repeat (1)
    metal(zinc)-bound alpha+beta fold
    1. Inhibitor of apoptosis (IAP) repeat (1)
53. TAZ domain (1)
    all-alpha fold; Zn-binding sites are in the loops connecting helices
    1. TAZ domain (1)
54. Cysteine-rich domain of the chaperone protein DnaJ. (1)
    metal(zinc)-bound extended beta-hairpin fold
    1. Cysteine-rich domain of the chaperone protein DnaJ. (1)