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
   1. Insulin-like [56994] (1)
      uperfamily
2. Knottins (small inhibitors, toxins, lectins) [57015] (19)
   disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
   1. Plant lectins/antimicrobial peptides [57016] (2)
      uperfamily
   2. Plant inhibitors of proteinases and amylases [57027] (1)
      uperfamily
   3. Cyclotides [57038] (4)
      macrocyclic plant knottins closed with the formation of an Asn-Gly peptide
      uperfamily
   4. Gurmarin-like [57048] (2)
      uperfamily
   5. Agouti-related protein [57055] (1)
      uperfamily
   6. omega toxin-like [57059] (5)
      uperfamily
   7. Scorpion toxin-like [57095] (5)
      uperfamily
   8. Cellulose-binding domain [57180] (1)
      uperfamily
   9. Growth factor receptor domain [57184] (1)
      uperfamily
   10. Colipase-like [57190] (1)
       uperfamily
   11. EGF/Laminin [57196] (7)
       uperfamily
   12. Bromelain inhibitor VI (cysteine protease inhibitor) [57243] (1)
       uperfamily
   13. Bowman-Birk inhibitor, BBI [57247] (1)
       uperfamily
   14. Elafin-like [57256] (1)
       uperfamily
   15. Leech antihemostatic proteins [57262] (2)
       uperfamily
   16. Granulin repeat [57277] (1)
       uperfamily
   17. Satiety factor CART (cocaine and amphetamine regulated transcript) [64546] (1)
       uperfamily
   18. DPY module [90148] (1)
       uperfamily
   19. Bubble protein [103565] (1)
       uperfamily
3. PMP inhibitors [57282] (1)
   disulfide-rich fold; all-beta: 3 antiparallel strands
   1. PMP inhibitors [57283] (1)
      uperfamily
4. Midkine [57287] (1)
   disulfide-rich fold; all-beta: 3 antiparallel strands
   1. Midkine [57288] (2)
      uperfamily
5. TSP-1 type 1 repeat [82894] (1)
   disulfide-rich fold; all-beta: 3 antiparallel strands
   1. TSP-1 type 1 repeat [82895] (1)
      uperfamily
6. Amb V allergen [57295] (1)
   disulfide-rich; alpha+beta: 3 antiparallel strands followed by a short alpha helix
   1. Amb V allergen [57296] (1)
      uperfamily
7. Snake toxin-like [57301] (1)
   disulfide-rich fold: nearly all-beta
   1. Snake toxin-like [57302] (3)
      uperfamily
8. BPTI-like [57361] (1)
   disulfide-rich alpha+beta fold
   1. BPTI-like [57362] (3)
      uperfamily
9. Defensin-like [57391] (1)
   Disulfide-rich fold, nearly all-beta
   1. Defensin-like [57392] (3)
      uperfamily
10. Hairpin loop containing domain-like [57413] (1)
    alpha+beta fold with two crossing loops
    1. Hairpin loop containing domain-like [57414] (3)
       the middle part is structurally similar to some knottins and defensins but differs in the disulfide pattern
       uperfamily
11. Neurotoxin III (ATX III) [57418] (1)
    disulfide-rich fold
    1. Neurotoxin III (ATX III) [57419] (1)
       uperfamily
12. LDL receptor-like module [57423] (1)
    disulfide-rich calcium-binding fold
    1. LDL receptor-like module [57424] (1)
       uperfamily
13. Crambin-like [57428] (1)
    disulfide-rich alpha+beta fold
    1. Crambin-like [57429] (1)
       uperfamily
14. Kringle-like [57439] (1)
    disulfide-rich fold; nearly all-beta
    1. Kringle-like [57440] (2)
       uperfamily
15. Kazal-type serine protease inhibitors [100894] (1)
    1. Kazal-type serine protease inhibitors [100895] (2)
       conserved core consists of a helix and a loop crosslinked with two disulfides
       uperfamily
16. Plant proteinase inhibitors [100896] (1)
    disulfide-rich small alpha+beta fold; topological similarity to the Ovomucoid domain III
    1. Plant proteinase inhibitors [100897] (1)
       uperfamily
17. Trefoil/Plexin domain-like [57491] (3)
    disulfide-rich fold; common core is alpha+beta with two conserved disulfides
    1. Trefoil [57492] (1)
       uperfamily
    2. Plexin repeat [103575] (1)
       uperfamily
    3. Variant surface glycoprotein MITAT 1.2, VSG 221, C-terminal domain [118251] (1)
       alpha-beta(2)-alpha; fragment of a larger dimeric protein
       uperfamily
18. Necrosis inducing protein 1, NIP1 [103579] (1)
    disulfide-rich fold; all-beta; duplication: contains two structural repeats
    1. Necrosis inducing protein 1, NIP1 [103580] (1)
       uperfamily
19. Cystine-knot cytokines [57500] (1)
    disulfide-rich fold; common core is all-beta
    1. Cystine-knot cytokines [57501] (7)
       uperfamily
20. Complement control module/SCR domain [57534] (1)
    disulfide-rich all-beta fold
    1. Complement control module/SCR domain [57535] (1)
       uperfamily
21. Crisp domain-like [57545] (1)
    disulfide-rich all-alpha fold
    1. Crisp domain-like [57546] (2)
       uperfamily
22. Blood coagulation inhibitor (disintegrin) [57551] (1)
    small disulfide-rich
    1. Blood coagulation inhibitor (disintegrin) [57552] (1)
       uperfamily
23. Methylamine dehydrogenase, L chain [57560] (1)
    disulfide-rich; nearly all-beta
    1. Methylamine dehydrogenase, L chain [57561] (1)
       uperfamily
24. Serine protease inhibitors [57566] (1)
    disulfide-rich; nearly all-beta
    1. Serine protease inhibitors [57567] (2)
       uperfamily
25. TB module/8-cys domain [57580] (1)
    disulfide-rich; alpha+beta
    1. TB module/8-cys domain [57581] (1)
       uperfamily
26. TNF receptor-like [57585] (1)
    duplication: consists of three similar disulfide-rich domains
    1. TNF receptor-like [57586] (2)
       uperfamily
27. Heparin-binding domain from vascular endothelial growth factor [57592] (1)
    duplication: consists of two similar disulfide-rich domains, alpha+beta
    1. Heparin-binding domain from vascular endothelial growth factor [57593] (1)
       uperfamily
28. Antifungal protein (AGAFP) [57597] (1)
    disulfide-rich; all-beta: open barrel, 5 strands; OB-fold-like
    1. Antifungal protein (AGAFP) [57598] (1)
       uperfamily
29. FnI-like domain [57602] (1)
    disulfide-rich, all-beta
    1. FnI-like domain [57603] (2)
       uperfamily
30. Thyroglobulin type-1 domain [57609] (1)
    disulfide-rich, alpha+beta
    1. Thyroglobulin type-1 domain [57610] (1)
       uperfamily
31. Type X cellulose binding domain, CBDX [57614] (1)
    disulfide-rich, alpha+beta
    1. Type X cellulose binding domain, CBDX [57615] (1)
       uperfamily
32. Cellulose docking domain, dockering [64570] (1)
    disulfide-rich, alpha+beta
    1. Cellulose docking domain, dockering [64571] (1)
       uperfamily
33. Carboxypeptidase inhibitor [57619] (1)
    disulfide-rich, alpha+beta
    1. Carboxypeptidase inhibitor [57620] (1)
       uperfamily
34. Invertebrate chitin-binding proteins [57624] (1)
    disulfide-rich
    1. Invertebrate chitin-binding proteins [57625] (2)
       shares a putative chitin-binding motif with the plant lectins/antimicrobial peptides superfamily but lacks one of the conserved disulfides of the knottin fold
       uperfamily
35. Pheromone ER-23 [69963] (1)
    disulfide-rich, all-alpha
    1. Pheromone ER-23 [69964] (1)
       uperfamily
36. Mollusk pheromone [90182] (1)
    disulfide-rich; all-alpha
    1. Mollusk pheromone [90183] (1)
       uperfamily
37. Apical membrane antigen 1 [82909] (1)
    disulfide-rich, alpha+beta
    1. Apical membrane antigen 1 [82910] (1)
       uperfamily
38. Somatomedin B domain [90187] (1)
    disulfide-rich
    1. Somatomedin B domain [90188] (1)
       uperfamily
39. Notch domain [90192] (1)
    disulfide-rich; all-alpha; calcium-binding
    1. Notch domain [90193] (1)
       uperfamily
40. Mini-collagen I, C-terminal domain [103588] (1)
    disulfide-rich
    1. Mini-collagen I, C-terminal domain [103589] (1)
       uperfamily
41. Hormone receptor domain [111417] (1)
    disulfide-rich all-beta fold; contains beta sandwich of 5 strands
    1. Hormone receptor domain [111418] (1)
       uperfamily
42. Resistin [111422] (1)
    disulfide-rich six-stranded beta-sandwich; jelly-roll
    1. Resistin [111423] (1)
       uperfamily
43. YAP1 redox domain [111429] (1)
    bipartite cysteine-rich all-alpha domain; a single helix in the N-terminal part (chain A) is linked by disulfides to the C-terminal part (chain B) [3-helical bundle of the RuvA C-terminal domain-like fold (scop_cf 46928)
    1. YAP1 redox domain [111430] (1)
       uperfamily
44. Toxic hairpin [57006] (4)
    disulfide crosslinked alpha-helical hairpin
    1. Heat-stable enterotoxin B [57007] (1)
       uperfamily
    2. Neurotoxin B-IV [57011] (1)
       uperfamily
    3. Pollen allergen ole e 6 [111388] (1)
       contains 3 disulfides
       uperfamily
    4. VhTI-like [161148] (1)
45. Tim10-like [144121] (1)
    alpha-hairpin crosslinked by two disulfides; assembles into a heterohexameric ring-like structure
    1. Tim10-like [144122] (1)
       uperfamily
46. Cysteine zipper [144128] (1)
    string of helices that contain cysteines at almost every turn; folds upon itself and is crosslnked by multiple disulfides
    1. Vanabin-like [144129] (1)
       uperfamily
47. GLA-domain [57629] (1)
    Calcium ion-bound
    1. GLA-domain [57630] (1)
       gamma-carboxy-glutamic acid-rich domain
       uperfamily
48. Cholecystokinin A receptor, N-domain [57641] (1)
    a few helical turns and a disulfide-crosslinked loop
    1. Cholecystokinin A receptor, N-domain [57642] (1)
       uperfamily
49. HIV-1 VPU cytoplasmic domain [57646] (1)
    a few helical turns assembled without a hydrophobic core?
    1. HIV-1 VPU cytoplasmic domain [57647] (1)
       uperfamily
50. HIPIP (high potential iron protein) [57651] (1)
    folds around 4Fe-4S cluster
    1. HIPIP (high potential iron protein) [57652] (1)
       uperfamily
51. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57661] (1)
    folds around 4Fe-4S cluster
    1. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57662] (1)
       uperfamily
52. beta-beta-alpha zinc fingers [57666] (1)
    simple fold, consisting of the N-terminal beta-hairpin and C-terminal alpha-helical region; each part provides two zinc-coordinating residues with the observed sequences including C2H2, C2HC and CHHC
    1. beta-beta-alpha zinc fingers [57667] (7)
       uperfamily
53. Zn2/Cys6 DNA-binding domain [57700] (1)
    all-alpha dimetal(zinc)-bound fold
    1. Zn2/Cys6 DNA-binding domain [57701] (1)
       duplication: two structural repeats are related by the pseudo dyad
       uperfamily
54. Glucocorticoid receptor-like (DNA-binding domain) [57715] (1)
    alpha+beta metal(zinc)-bound fold
    1. Glucocorticoid receptor-like (DNA-binding domain) [57716] (18)
       uperfamily
55. SBT domain [103611] (1)
    consist of two different zn-binding subdomains, each subdomain resembles a distorted glucocorticoid receptor-like fold
    1. SBT domain [103612] (1)
       uperfamily
56. Retrovirus zinc finger-like domains [57755] (1)
    metal(zinc)-bound fold
    1. Retrovirus zinc finger-like domains [57756] (1)
       uperfamily
57. Rubredoxin-like [57769] (17)
    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 [57770] (1)
       uperfamily
    2. Microbial and mitochondrial ADK, insert "zinc finger" domain [57774] (1)
       uperfamily
    3. NADH pyrophosphatase intervening domain [116738] (1)
       uperfamily
    4. Zinc beta-ribbon [57783] (5)
       uperfamily
    5. Casein kinase II beta subunit [57798] (1)
       uperfamily
    6. Rubredoxin-like [57802] (3)
       uperfamily
    7. Zn-finger domain of Sec23/24 [82919] (1)
       uperfamily
    8. Ran binding protein zinc finger-like [90209] (1)
       contains CxxxxC-x(n)-CxxC zinc-binding site; similar to the Sec23/24 zinc finger domain
       uperfamily
    9. Hypothetical protein Ta0289 C-terminal domain [103623] (1)
       contains CxxC-x(n)-CxxxxC zinc-binding site; sequence similarity to NAD-dependent DNA ligase zinc-finger subdomain
       uperfamily
    10. Hypothetical protein MTH1184 [57821] (1)
        contains two CXC motifs
        uperfamily
    11. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57825] (1)
        uperfamily
    12. Zn-binding ribosomal proteins [57829] (8)
        uperfamily
    13. RNA polymerase subunits [63393] (2)
        uperfamily
    14. NOB1 zinc finger-like [144206] (1)
        uperfamily
    15. Nop10-like SnoRNP [144210] (1)
        uperfamily
    16. CSL zinc finger [144217] (1)
        uperfamily
    17. YfgJ-like [161187] (1)
        duplication: consists of two rubredoxin-like (sub)domains, interlocked together
58. Ribosomal protein L36 [57839] (1)
    zinc-bound beta-ribbon motif
    1. Ribosomal protein L36 [57840] (1)
       uperfamily
59. Zinc-binding domain of translation initiation factor 2 beta [75688] (1)
    zinc-bound beta-ribbon motif
    1. Zinc-binding domain of translation initiation factor 2 beta [75689] (1)
       uperfamily
60. WRKY DNA-binding domain [118289] (1)
    zinc-bound 4-stranded meander beta-sheet, distinct from the beta-ribbon motifs
    1. WRKY DNA-binding domain [118290] (1)
       uperfamily
61. B-box zinc-binding domain [57844] (1)
    zinc-bound alpha+beta motif
    1. B-box zinc-binding domain [57845] (1)
       uperfamily
62. RING/U-box [57849] (1)
    dimetal(zinc)-bound alpha+beta motif; structurally diverse
    1. RING/U-box [57850] (6)
       uperfamily
63. ArfGap/RecO-like zinc finger [57862] (1)
    zinc-bound alpha+beta motif
    1. ArfGap/RecO-like zinc finger [57863] (2)
       uperfamily
64. Metallothionein [57867] (1)
    metal(iron)-bound fold
    duplication: consists of clear structural/sequence repeats
    1. Metallothionein [57868] (1)
       uperfamily
65. Zinc domain conserved in yeast copper-regulated transcription factors [57878] (1)
    metal(zinc)-bound alpha+beta fold
    1. Zinc domain conserved in yeast copper-regulated transcription factors [57879] (1)
       uperfamily
66. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57883] (1)
    metal(zinc)-bound alpha+beta fold
    1. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57884] (1)
       uperfamily
67. Cysteine-rich domain [57888] (1)
    dimetal(zinc)-bound alpha+beta fold
    1. Cysteine-rich domain [57889] (3)
       uperfamily
68. AN1-like Zinc finger [118309] (1)
    dimetal(zinc)-bound alpha+beta fold; partial similarity to the Cysteine-rich domain fold (scop_cf 57888)
    1. AN1-like Zinc finger [118310] (1)
       uperfamily
69. HIT/MYND zinc finger-like [144231] (1)
    dimetal(zinc)-bound alpha+beta fold; structural similarity to members of the Cysteine-rich domain fold (scop_cf 57888)
    1. HIT/MYND zinc finger-like [144232] (2)
       uperfamily
70. CHY zinc finger-like [161218] (1)
    trimetal-bound fold; integration of HIT/MYND-like and rubredoxin-like fingers
    1. CHY zinc finger-like [161219] (1)
71. FYVE/PHD zinc finger [57902] (1)
    dimetal(zinc)-bound alpha+beta fold
    1. FYVE/PHD zinc finger [57903] (3)
       uperfamily
72. Zn-binding domains of ADDBP [57916] (1)
    metal(zinc)-bound alpha+beta fold
    1. Zn-binding domains of ADDBP [57917] (1)
       duplication: contains two Zn-binding domains of similar fold
       uperfamily
73. Inhibitor of apoptosis (IAP) repeat [57923] (1)
    metal(zinc)-bound alpha+beta fold
    1. Inhibitor of apoptosis (IAP) repeat [57924] (1)
       uperfamily
74. CCCH zinc finger [90228] (1)
    metal(zinc)-bound alpha+beta fold
    1. CCCH zinc finger [90229] (1)
       uperfamily
75. E6 C-terminal domain-like [161228] (1)
    alpha+beta zinc-binding fold with topological similarity to the fold of lambda cro protein
    1. E6 C-terminal domain-like [161229] (1)
76. E7 C-terminal domain-like [161233] (1)
    alpha+beta zinc-binding domain; beta(2)-alpha(2)
    1. E7 C-terminal domain-like [161234] (1)
77. Zinc finger domain of DNA polymerase-alpha [90233] (1)
    Zn-binding, all-alpha fold
    1. Zinc finger domain of DNA polymerase-alpha [90234] (1)
       some sequence similarity to the TAZ domain Zn-binding sites
       uperfamily
78. TAZ domain [57932] (1)
    all-alpha fold; Zn-binding sites are in the loops connecting helices
    1. TAZ domain [57933] (1)
       uperfamily
79. T-antigen specific domain-like [161239] (1)
    all-alpha zinc-binding domain; there are two zinc ion-binding sites with a common CxCxxC motif but different fourth ligands
    1. T-antigen specific domain-like [161240] (1)
80. Cysteine-rich DNA binding domain, (DM domain) [82926] (1)
    alpha-helical fold with two Zn-binding sites
    1. Cysteine-rich DNA binding domain, (DM domain) [82927] (1)
       uperfamily
81. Coronavirus NSP10-like [144245] (1)
    binds two zinc ion per subunit; forms a dodecameric shell
    1. Coronavirus NSP10-like [144246] (1)
       uperfamily
82. Zinc hairpin stack [161244] (1)
    stack of beta-hairpins; in the middle hairpins, there is HCxxCxxC motif, the first and the last residues of which contribute to the zinc-binding site on one side of hairpin, whereas the middle residues contribute to the zinc-binding site on the other side
    1. Zinc hairpin stack [161245] (1)
83. DnaJ/Hsp40 cysteine-rich domain [57937] (1)
    metal(zinc)-bound extended beta-hairpin fold
    1. DnaJ/Hsp40 cysteine-rich domain [57938] (1)
       uperfamily
84. HSP33 redox switch-like [118351] (1)
    alpha+beta zinc-binding domain; alpha(2)-beta(2)-alpha
    1. HSP33 redox switch-like [118352] (1)
       uperfamily
85. CCHHC domain [103636] (1)
    metal(zinc)-bound fold
    1. CCHHC domain [103637] (1)
       uperfamily
86. Sec-C motif [103641] (1)
    metal(zinc)-bound fold
    1. Sec-C motif [103642] (1)
       uperfamily
87. Viral leader polypeptide zinc finger [144250] (1)
    consists of small beta-hairpin with CxH motif and short helix with CxxC motif
    1. Viral leader polypeptide zinc finger [144251] (1)
       uperfamily
88. TSP type-3 repeat [103646] (1)
    metal(calcium)-bound fold
    1. TSP type-3 repeat [103647] (1)
       uperfamily
89. Expressed protein At2g23090/F21P24.15 [118358] (1)
    not assigned; partly disordered
    1. Expressed protein At2g23090/F21P24.15 [118359] (1)
       putative zinc-finger protein
       uperfamily
90. Intrinsically disordered proteins [144255] (1)
    not a true fold
    1. TSP9-like [144256] (1)
       uperfamily

Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009 Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk