Structural Classification of Proteins

Class: Small proteins

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

Lineage:

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

Folds:

Insulin-like [56993] (1)
nearly all-alpha
can be classified as disulfide-rich
1. Insulin-like [56994] (1)
  uperfamily
  1. Insulin-like [56995] (6)
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
  1. Hevein-like agglutinin (lectin) domain [57017] (6)
  2. Antimicrobial peptide 2, AC-AMP2 [57024] (1)
2. Plant inhibitors of proteinases and amylases [57027] (1)
  uperfamily
  1. Plant inhibitors of proteinases and amylases [57028] (7)
3. Cyclotides [57038] (4)
  macrocyclic plant knottins closed with the formation of an Asn-Gly peptide
  uperfamily
  1. Kalata B1 [57039] (1)
  2. Cycloviolacin [57042] (2)
  3. Circulin A [57045] (1)
  4. Palicourein [103526] (1)
4. Gurmarin-like [57048] (2)
  uperfamily
  1. Gurmarin, a sweet taste-suppressing polypeptide [57049] (1)
  2. Antifungal peptide [57052] (2)
5. Agouti-related protein [57055] (1)
  uperfamily
  1. Agouti-related protein [57056] (1)
6. omega toxin-like [57059] (5)
  uperfamily
  1. Conotoxin [57060] (13)
  2. Spider toxins [57072] (25)
  3. Insect toxins [69930] (2)
  4. Albumin 1 [90134] (2)
  5. Vhv1.1, polydnaviral gene product [118237] (1)
7. Scorpion toxin-like [57095] (5)
  uperfamily
  1. Long-chain scorpion toxins [57096] (22)
  2. Short-chain scorpion toxins [57116] (38)
  3. Defensin MGD-1 [57160] (1)
  4. Insect defensins [57163] (6)
  5. Plant defensins [57170] (10)
8. Cellulose-binding domain [57180] (1)
  uperfamily
  1. Cellulose-binding domain [57181] (1)
9. Growth factor receptor domain [57184] (1)
  uperfamily
  1. Growth factor receptor domain [57185] (9)
10. Colipase-like [57190] (1)
  uperfamily
  1. Colipase-like [57191] (2)
11. EGF/Laminin [57196] (7)
  uperfamily
  1. EGF-type module [57197] (27)
  2. Integrin beta EGF-like domains [69940] (1)
  3. EGF-like domain of nidogen-1 [64541] (1)
  4. Laminin-type module [57233] (1)
  5. Follistatin (FS) module N-terminal domain, FS-N [57236] (2)
  6. Merozoite surface protein 1 (MSP-1) [57239] (3)
  7. Cripto EGF-like domain-like [144100] (1)
12. Bromelain inhibitor VI (cysteine protease inhibitor) [57243] (1)
  uperfamily
  1. Bromelain inhibitor VI (cysteine protease inhibitor) [57244] (1)
13. Bowman-Birk inhibitor, BBI [57247] (1)
  uperfamily
  1. Bowman-Birk inhibitor, BBI [57248] (10)
14. Elafin-like [57256] (1)
  uperfamily
  1. Elafin-like [57257] (2)
15. Leech antihemostatic proteins [57262] (2)
  uperfamily
  1. Huristasin-like [57263] (3)
  2. Hirudin-like [57270] (3)
16. Granulin repeat [57277] (1)
  uperfamily
  1. Granulin repeat [57278] (3)
17. Satiety factor CART (cocaine and amphetamine regulated transcript) [64546] (1)
  uperfamily
  1. Satiety factor CART (cocaine and amphetamine regulated transcript) [64547] (1)
18. DPY module [90148] (1)
  uperfamily
  1. DPY module [90149] (1)
19. Bubble protein [103565] (1)
  uperfamily
  1. Bubble protein [103566] (1)
PMP inhibitors [57282] (1)
disulfide-rich fold; all-beta: 3 antiparallel strands
1. PMP inhibitors [57283] (1)
  uperfamily
  1. PMP inhibitors [57284] (4)
Midkine [57287] (1)
disulfide-rich fold; all-beta: 3 antiparallel strands
1. Midkine [57288] (2)
  uperfamily
  1. Midkine, a heparin-binding growth factor, N-terminal domain [57289] (1)
  2. Midkine, a heparin-binding growth factor, C-terminal domain [57292] (1)
TSP-1 type 1 repeat [82894] (1)
disulfide-rich fold; all-beta: 3 antiparallel strands
1. TSP-1 type 1 repeat [82895] (1)
  uperfamily
  1. TSP-1 type 1 repeat [82896] (1)
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
  1. Amb V allergen [57297] (1)
Snake toxin-like [57301] (1)
disulfide-rich fold: nearly all-beta
1. Snake toxin-like [57302] (3)
  uperfamily
  1. Snake venom toxins [57303] (36)
  2. Dendroaspin [57351] (1)
  3. Extracellular domain of cell surface receptors [57354] (9)
BPTI-like [57361] (1)
disulfide-rich alpha+beta fold
1. BPTI-like [57362] (3)
  uperfamily
  1. Small Kunitz-type inhibitors & BPTI-like toxins [57363] (12)
  2. Soft tick anticoagulant proteins [57386] (2)
  3. Tick tryptase inhibitor-like [161132] (1)
Defensin-like [57391] (1)
Disulfide-rich fold, nearly all-beta
1. Defensin-like [57392] (3)
  uperfamily
  1. Defensin [57393] (17)
  2. Myotoxin [90157] (1)
    structurally similar to beta-defensin
  3. Tick carboxypeptidase inhibitor-like [161135] (1)
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
  1. Hairpin loop containing domain [57415] (1)
  2. Anti-platelet protein [64556] (1)
  3. Pan module (APPLE domain) [82901] (1)
    probable carbohydrate-binding function
Neurotoxin III (ATX III) [57418] (1)
disulfide-rich fold
1. Neurotoxin III (ATX III) [57419] (1)
  uperfamily
  1. Neurotoxin III (ATX III) [57420] (1)
LDL receptor-like module [57423] (1)
disulfide-rich calcium-binding fold
1. LDL receptor-like module [57424] (1)
  uperfamily
  1. LDL receptor-like module [57425] (6)
Crambin-like [57428] (1)
disulfide-rich alpha+beta fold
1. Crambin-like [57429] (1)
  uperfamily
  1. Crambin-like [57430] (9)
Kringle-like [57439] (1)
disulfide-rich fold; nearly all-beta
1. Kringle-like [57440] (2)
  uperfamily
  1. Kringle modules [57441] (9)
  2. Fibronectin type II module [57459] (4)
    shorter two-disulfide version of a kringle module
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
  1. Ovomucoid domain III-like [57468] (14)
  2. Serine proteinase inhibitor lekti [69960] (1)
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
  1. Plant proteinase inhibitors [57486] (3)
Trefoil/Plexin domain-like [57491] (3)
disulfide-rich fold; common core is alpha+beta with two conserved disulfides
1. Trefoil [57492] (1)
  uperfamily
  1. Trefoil [57493] (3)
2. Plexin repeat [103575] (1)
  uperfamily
  1. Plexin repeat [103576] (3)
    Pfam 01437
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
  1. Variant surface glycoprotein MITAT 1.2, VSG 221, C-terminal domain [118252] (1)
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
  1. Necrosis inducing protein 1, NIP1 [103581] (1)
Cystine-knot cytokines [57500] (1)
disulfide-rich fold; common core is all-beta
1. Cystine-knot cytokines [57501] (7)
  uperfamily
  1. Platelet-derived growth factor-like [57502] (5)
  2. Transforming growth factor (TGF)-beta [57507] (7)
  3. Noggin [82904] (1)
  4. Neurotrophin [57520] (5)
  5. Gonadodropin/Follitropin [57528] (3)
  6. Interleukin 17F, IL-17F [69955] (1)
  7. Coagulogen [57531] (1)
Complement control module/SCR domain [57534] (1)
disulfide-rich all-beta fold
1. Complement control module/SCR domain [57535] (1)
  uperfamily
  1. Complement control module/SCR domain [57536] (15)
    Pfam 00084
Crisp domain-like [57545] (1)
disulfide-rich all-alpha fold
1. Crisp domain-like [57546] (2)
  uperfamily
  1. Sea anemone toxin k [57547] (2)
  2. Crisp domain [118259] (1)
    Pfam 08562; contains extra N-terminal knottin-like subdomain
Blood coagulation inhibitor (disintegrin) [57551] (1)
small disulfide-rich
1. Blood coagulation inhibitor (disintegrin) [57552] (1)
  uperfamily
  1. Blood coagulation inhibitor (disintegrin) [57553] (6)
Methylamine dehydrogenase, L chain [57560] (1)
disulfide-rich; nearly all-beta
1. Methylamine dehydrogenase, L chain [57561] (1)
  uperfamily
  1. Methylamine dehydrogenase, L chain [57562] (2)
Serine protease inhibitors [57566] (1)
disulfide-rich; nearly all-beta
1. Serine protease inhibitors [57567] (2)
  uperfamily
  1. ATI-like [57568] (4)
  2. BSTI [57577] (1)
TB module/8-cys domain [57580] (1)
disulfide-rich; alpha+beta
1. TB module/8-cys domain [57581] (1)
  uperfamily
  1. TB module/8-cys domain [57582] (2)
    transforming growth factor beta binding protein-like domain
TNF receptor-like [57585] (1)
duplication: consists of three similar disulfide-rich domains
1. TNF receptor-like [57586] (2)
  uperfamily
  1. TNF receptor-like [57587] (5)
    Pfam 00020; TNFR/NGFR cysteine-rich region
  2. BAFF receptor-like [90174] (3)
    only fragments of the receptor structures are available; no domain division is provided here
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
  1. Heparin-binding domain from vascular endothelial growth factor [57594] (1)
Antifungal protein (AGAFP) [57597] (1)
disulfide-rich; all-beta: open barrel, 5 strands; OB-fold-like
1. Antifungal protein (AGAFP) [57598] (1)
  uperfamily
  1. Antifungal protein (AGAFP) [57599] (1)
FnI-like domain [57602] (1)
disulfide-rich, all-beta
1. FnI-like domain [57603] (2)
  uperfamily
  1. Fibronectin type I module [57604] (2)
  2. VWC domain [118264] (1)
    Pfam 00093; similar to FnI domain in the N-terminal part, contains extra C-terminal subdomain
Thyroglobulin type-1 domain [57609] (1)
disulfide-rich, alpha+beta
1. Thyroglobulin type-1 domain [57610] (1)
  uperfamily
  1. Thyroglobulin type-1 domain [57611] (4)
    Pfam 00086
Type X cellulose binding domain, CBDX [57614] (1)
disulfide-rich, alpha+beta
1. Type X cellulose binding domain, CBDX [57615] (1)
  uperfamily
  1. Type X cellulose binding domain, CBDX [57616] (1)
Cellulose docking domain, dockering [64570] (1)
disulfide-rich, alpha+beta
1. Cellulose docking domain, dockering [64571] (1)
  uperfamily
  1. Cellulose docking domain, dockering [64572] (1)
Carboxypeptidase inhibitor [57619] (1)
disulfide-rich, alpha+beta
1. Carboxypeptidase inhibitor [57620] (1)
  uperfamily
  1. Carboxypeptidase inhibitor [57621] (1)
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
  1. Tachycitin [57626] (1)
  2. Antifungal peptide scarabaecin [90179] (1)
Pheromone ER-23 [69963] (1)
disulfide-rich, all-alpha
1. Pheromone ER-23 [69964] (1)
  uperfamily
  1. Pheromone ER-23 [69965] (1)
Mollusk pheromone [90182] (1)
disulfide-rich; all-alpha
1. Mollusk pheromone [90183] (1)
  uperfamily
  1. Mollusk pheromone [90184] (1)
Apical membrane antigen 1 [82909] (1)
disulfide-rich, alpha+beta
1. Apical membrane antigen 1 [82910] (1)
  uperfamily
  1. Apical membrane antigen 1 [82911] (1)
Somatomedin B domain [90187] (1)
disulfide-rich
1. Somatomedin B domain [90188] (1)
  uperfamily
  1. Somatomedin B domain [90189] (1)
Notch domain [90192] (1)
disulfide-rich; all-alpha; calcium-binding
1. Notch domain [90193] (1)
  uperfamily
  1. Notch domain [90194] (1)
    also called DSL domain or LNR repeat
Mini-collagen I, C-terminal domain [103588] (1)
disulfide-rich
1. Mini-collagen I, C-terminal domain [103589] (1)
  uperfamily
  1. Mini-collagen I, C-terminal domain [103590] (1)
Hormone receptor domain [111417] (1)
disulfide-rich all-beta fold; contains beta sandwich of 5 strands
1. Hormone receptor domain [111418] (1)
  uperfamily
  1. Hormone receptor domain [111419] (2)
    Pfam 02793; HRM
Resistin [111422] (1)
disulfide-rich six-stranded beta-sandwich; jelly-roll
1. Resistin [111423] (1)
  uperfamily
  1. Resistin [111424] (2)
    Pfam 06954
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
  1. YAP1 redox domain [111431] (1)
Toxic hairpin [57006] (4)
disulfide crosslinked alpha-helical hairpin
1. Heat-stable enterotoxin B [57007] (1)
  uperfamily
  1. Heat-stable enterotoxin B [57008] (1)
    contains 2 disulfides
2. Neurotoxin B-IV [57011] (1)
  uperfamily
  1. Neurotoxin B-IV [57012] (1)
    contains 4 disulfides
3. Pollen allergen ole e 6 [111388] (1)
  contains 3 disulfides
  uperfamily
  1. Pollen allergen ole e 6 [111389] (1)
4. VhTI-like [161148] (1)
  1. VhTI-like [161149] (1)
Tim10-like [144121] (1)
alpha-hairpin crosslinked by two disulfides; assembles into a heterohexameric ring-like structure
1. Tim10-like [144122] (1)
  uperfamily
  1. Tim10/DDP [144123] (2)
    Pfam 02953; note: not a zinc finger
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
  1. Vanabin-like [144130] (1)
GLA-domain [57629] (1)
Calcium ion-bound
1. GLA-domain [57630] (1)
  gamma-carboxy-glutamic acid-rich domain
  uperfamily
  1. GLA-domain [57631] (9)
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
  1. Cholecystokinin A receptor, N-domain [57643] (1)
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
  1. HIV-1 VPU cytoplasmic domain [57648] (1)
HIPIP (high potential iron protein) [57651] (1)
folds around 4Fe-4S cluster
1. HIPIP (high potential iron protein) [57652] (1)
  uperfamily
  1. HIPIP (high potential iron protein) [57653] (7)
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
  1. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57663] (1)
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
  1. Classic zinc finger, C2H2 [57668] (30)
  2. Plant C2H2 finger (QALGGH zinc finger) [90198] (1)
  3. C2HC finger [57697] (3)
  4. HkH motif-containing C2H2 finger [111436] (4)
    putative dsRNA-specific zinc finger with a helix-kink-helix (HkH) motif; the kink results from the incompatibility of the cation-coordinating H-x5-H motif with a regular alpha-helix and contributes to RNA recognition
  5. CHHC finger [161158] (1)
  6. variant C2H2 finger [118273] (1)
    contains extra C-terminal, alpha-helical subdomain
  7. BED zinc finger [144157] (1)
    Pfam 02892; contains extra N-terminal and C-terminal helices bundled together with the core helix
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
  1. Zn2/Cys6 DNA-binding domain [57702] (6)
Glucocorticoid receptor-like (DNA-binding domain) [57715] (1)
alpha+beta metal(zinc)-bound fold
1. Glucocorticoid receptor-like (DNA-binding domain) [57716] (18)
  uperfamily
  1. Erythroid transcription factor GATA-1 [57717] (3)
    single zinc-binding motif
  2. Nuclear receptor [57721] (12)
    duplication: two zinc-binding motifs
  3. Transcription factor grauzone Cg33133-Pa, zinc finger associated domain [103605] (1)
  4. LIM domain [57736] (21)
    duplication: contains two (sub)domains of this fold
  5. LASP-1 [57743] (1)
  6. DNA repair factor XPA DNA- and RPA-binding domain, N-terminal subdomain [57746] (1)
  7. Ribosomal protein L24e [57749] (1)
  8. Hypothetical zinc finger protein YacG [82914] (1)
    Zn-binding site is particularly similar to that of ribosomal protein L24e
  9. Ribosomal protein S14 [57752] (2)
  10. C-terminal, Zn-finger domain of MutM-like DNA repair proteins [81627] (6)
  11. ClpX chaperone zinc binding domain [103608] (1)
  12. PARP-type zinc finger [111445] (1)
    Pfam 00645
  13. Prokaryotic DksA/TraR C4-type zinc finger [111448] (1)
    Pfam 01258; Pfam coverage extends to the second helix of the upstream alpha-hairpin domain
  14. Type II thymidine kinase zinc finger [118276] (3)
    C-terminal part of Pfam 00265
  15. A20-like zinc finger [144187] (2)
    Pfam 01754
  16. THAP domain [161163] (1)
    Pfam 05485
  17. TRASH domain [161166] (1)
    SMART 00746
  18. FwdE C-terminal domain-like [161169] (1)
    the C-terminus of PF02663; FwdE
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
  1. SBT domain [103613] (3)
    Pfam 03110
Retrovirus zinc finger-like domains [57755] (1)
metal(zinc)-bound fold
1. Retrovirus zinc finger-like domains [57756] (1)
  uperfamily
  1. Retrovirus zinc finger-like domains [57757] (6)
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
  1. Methionyl-tRNA synthetase (MetRS), Zn-domain [57771] (2)
    in the Pyrococcus abyssi MetRS structure there is a tandem repeat of two such domains swapped with their zinc-binding 'knuckles', this duplicated finger occupies a larger region (124-183) than defined below; there is a structurally equivalent region in the E. coli enzyme lacking the second zinc-binding site
2. Microbial and mitochondrial ADK, insert "zinc finger" domain [57774] (1)
  uperfamily
  1. Microbial and mitochondrial ADK, insert "zinc finger" domain [57775] (8)
3. NADH pyrophosphatase intervening domain [116738] (1)
  uperfamily
  1. NADH pyrophosphatase intervening domain [116739] (1)
4. Zinc beta-ribbon [57783] (5)
  uperfamily
  1. Transcriptional factor domain [57784] (6)
  2. DNA primase zinc finger [57792] (2)
    contains alpha-helices in the N- and C-terminal extensions (linkers?)
  3. Prokaryotic DNA topoisomerase I, a C-terminal fragment [57795] (1)
    Duplication: contains tandem repeats of several domains with zinc-binding sites being lost in some of them
  4. Putative zinc binding domain [118285] (1)
    Pfam 05129; DUF701
  5. PhnA zinc-binding domain [144191] (1)
    Pfam 08274
5. Casein kinase II beta subunit [57798] (1)
  uperfamily
  1. Casein kinase II beta subunit [57799] (3)
    contains alpha-helices in the N- and C-terminal extensions (linkers?)
6. Rubredoxin-like [57802] (3)
  uperfamily
  1. Rubredoxin [57803] (10)
  2. Desulforedoxin [57813] (3)
  3. Cytochrome c oxidase Subunit F [57818] (1)
    membrane-anchored rubredoxin-like domain
7. Zn-finger domain of Sec23/24 [82919] (1)
  uperfamily
  1. Zn-finger domain of Sec23/24 [82920] (2)
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
  1. Ran binding protein zinc finger-like [90210] (6)
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
  1. Hypothetical protein Ta0289 C-terminal domain [103624] (1)
10. Hypothetical protein MTH1184 [57821] (1)
  contains two CXC motifs
  uperfamily
  1. Hypothetical protein MTH1184 [57822] (1)
    possible metal-binding fold
11. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57825] (1)
  uperfamily
  1. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57826] (2)
12. Zn-binding ribosomal proteins [57829] (8)
  uperfamily
  1. Ribosomal protein L37ae [57830] (1)
  2. Ribosomal protein L37e [57833] (1)
  3. Ribosomal protein L44e [57836] (1)
  4. Ribosomal protein S27e [90217] (1)
  5. Ribosomal protein L32p [144200] (3)
    Pfam 01783; metal ion-binding site is lost in some members; includes the N-terminal, mainly helical tail
  6. Ribosomal protein L33p [144203] (3)
    Pfam 00471; corresponds structurally and functionally to the ribosomal L44e from eukaryota and archaea; metal ion-binding site is lost in most members
  7. Ribosomal protein L40e [161181] (1)
    Pfam 01020
  8. Ribosomal protein S27a [161184] (1)
    Pfam 01599
13. RNA polymerase subunits [63393] (2)
  uperfamily
  1. RBP12 subunit of RNA polymerase II [64576] (1)
  2. RpoE2-like [111454] (1)
    Pfam 04035
14. NOB1 zinc finger-like [144206] (1)
  uperfamily
  1. NOB1 zinc finger-like [144207] (1)
15. Nop10-like SnoRNP [144210] (1)
  uperfamily
  1. Nucleolar RNA-binding protein Nop10-like [144211] (3)
    Pfam 04135; contains N-terminal zinc-finger domain similar to the insert finger of the Initiation factor eIF2 gamma subunit (scop_pr 75204)
16. CSL zinc finger [144217] (1)
  uperfamily
  1. CSL zinc finger [144218] (2)
    Pfam 05207
17. YfgJ-like [161187] (1)
  duplication: consists of two rubredoxin-like (sub)domains, interlocked together
  1. YfgJ-like [161188] (1)
    Pfam 07191, DUF1407
Ribosomal protein L36 [57839] (1)
zinc-bound beta-ribbon motif
1. Ribosomal protein L36 [57840] (1)
  uperfamily
  1. Ribosomal protein L36 [57841] (3)
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
  1. Zinc-binding domain of translation initiation factor 2 beta [75690] (2)
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
  1. WRKY DNA-binding domain [118291] (1)
    Pfam 03106
B-box zinc-binding domain [57844] (1)
zinc-bound alpha+beta motif
1. B-box zinc-binding domain [57845] (1)
  uperfamily
  1. B-box zinc-binding domain [57846] (7)
RING/U-box [57849] (1)
dimetal(zinc)-bound alpha+beta motif; structurally diverse
1. RING/U-box [57850] (6)
  uperfamily
  1. RING finger domain, C3HC4 [57851] (14)
  2. U-box [90222] (4)
    Associated with multi-ubiquitination; lacks the RING-domain metal ion-binding residues
  3. Variant RING domain [118300] (2)
  4. IBR domain [144228] (1)
    Smart 00647; RING-associated domain
  5. Zf-UBP [161204] (3)
    Pfam 02148
  6. ZZ domain [161211] (3)
    Pfam 00569
ArfGap/RecO-like zinc finger [57862] (1)
zinc-bound alpha+beta motif
1. ArfGap/RecO-like zinc finger [57863] (2)
  uperfamily
  1. Pyk2-associated protein beta ARF-GAP domain [57864] (1)
  2. RecO C-terminal domain-like [118303] (1)
    C-terminal part of Pfam 02565
Metallothionein [57867] (1)
metal(iron)-bound fold
duplication: consists of clear structural/sequence repeats
1. Metallothionein [57868] (1)
  uperfamily
  1. Metallothionein [57869] (11)
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
  1. Zinc domain conserved in yeast copper-regulated transcription factors [57880] (1)
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
  1. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57885] (1)
Cysteine-rich domain [57888] (1)
dimetal(zinc)-bound alpha+beta fold
1. Cysteine-rich domain [57889] (3)
  uperfamily
  1. Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) [57890] (6)
    Pfam 00130
  2. TFIIH p44 subunit cysteine-rich domain [57899] (1)
  3. C1-like domain [111463] (1)
    contains Pfam 03107 (C1_2) and Pfam 07649 (C1_3)
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
  1. AN1-like Zinc finger [118311] (6)
    Pfam 01428
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
  1. MYND zinc finger [144233] (3)
    Pfam 01753
  2. HIT zinc finger [144240] (1)
    Pfam 04438
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)
  1. CHY zinc finger [161220] (1)
    Pfam 05495
FYVE/PHD zinc finger [57902] (1)
dimetal(zinc)-bound alpha+beta fold
1. FYVE/PHD zinc finger [57903] (3)
  uperfamily
  1. FYVE, a phosphatidylinositol-3-phosphate binding domain [57904] (6)
  2. PHD domain [57911] (14)
  3. variant PHD-like domain [118346] (1)
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
  1. Zn-binding domains of ADDBP [57918] (2)
Inhibitor of apoptosis (IAP) repeat [57923] (1)
metal(zinc)-bound alpha+beta fold
1. Inhibitor of apoptosis (IAP) repeat [57924] (1)
  uperfamily
  1. Inhibitor of apoptosis (IAP) repeat [57925] (7)
CCCH zinc finger [90228] (1)
metal(zinc)-bound alpha+beta fold
1. CCCH zinc finger [90229] (1)
  uperfamily
  1. CCCH zinc finger [90230] (4)
    C-x8-C-x5-C-x3-H type and similar
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)
  1. E6 C-terminal domain-like [161230] (1)
    C-terminal part of Pfam 00518
E7 C-terminal domain-like [161233] (1)
alpha+beta zinc-binding domain; beta(2)-alpha(2)
1. E7 C-terminal domain-like [161234] (1)
  1. E7 C-terminal domain-like [161235] (2)
    C-terminal part of Pfam 00527
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
  1. Zinc finger domain of DNA polymerase-alpha [90235] (1)
TAZ domain [57932] (1)
all-alpha fold; Zn-binding sites are in the loops connecting helices
1. TAZ domain [57933] (1)
  uperfamily
  1. TAZ domain [57934] (2)
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)
  1. T-antigen specific domain-like [161241] (1)
    Pfam 02380
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
  1. Cysteine-rich DNA binding domain, (DM domain) [82928] (1)
Coronavirus NSP10-like [144245] (1)
binds two zinc ion per subunit; forms a dodecameric shell
1. Coronavirus NSP10-like [144246] (1)
  uperfamily
  1. Coronavirus NSP10-like [144247] (1)
    partly covered by PfamB 001266
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)
  1. Zinc hairpin stack [161246] (1)
    PfamB 004087
DnaJ/Hsp40 cysteine-rich domain [57937] (1)
metal(zinc)-bound extended beta-hairpin fold
1. DnaJ/Hsp40 cysteine-rich domain [57938] (1)
  uperfamily
  1. DnaJ/Hsp40 cysteine-rich domain [57939] (2)
HSP33 redox switch-like [118351] (1)
alpha+beta zinc-binding domain; alpha(2)-beta(2)-alpha
1. HSP33 redox switch-like [118352] (1)
  uperfamily
  1. HSP33 redox switch-like [118353] (3)
CCHHC domain [103636] (1)
metal(zinc)-bound fold
1. CCHHC domain [103637] (1)
  uperfamily
  1. CCHHC domain [103638] (1)
Sec-C motif [103641] (1)
metal(zinc)-bound fold
1. Sec-C motif [103642] (1)
  uperfamily
  1. Sec-C motif [103643] (3)
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
  1. Viral leader polypeptide zinc finger [144252] (1)
TSP type-3 repeat [103646] (1)
metal(calcium)-bound fold
1. TSP type-3 repeat [103647] (1)
  uperfamily
  1. TSP type-3 repeat [103648] (1)
Expressed protein At2g23090/F21P24.15 [118358] (1)
not assigned; partly disordered
1. Expressed protein At2g23090/F21P24.15 [118359] (1)
  putative zinc-finger protein
  uperfamily
  1. Expressed protein At2g23090/F21P24.15 [118360] (1)
Intrinsically disordered proteins [144255] (1)
not a true fold
1. TSP9-like [144256] (1)
  uperfamily
  1. TSP9-like [144257] (1)