SCOP: Structural Classification of Proteins and ASTRAL

Structural Classification of Proteins and ASTRAL release 1.75B (January 2013)

Folds found:

c.2: NAD(P)-binding Rossmann-fold domains [51734] (1 superfamily)
core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456
The nucleotide-binding modes of this and the next two folds/superfamilies are similar
c.3: FAD/NAD(P)-binding domain [51904] (1 superfamily)
core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
c.4: Nucleotide-binding domain [51970] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
c.5: MurCD N-terminal domain [51983] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group
c.24: Methylglyoxal synthase-like [52334] (1 superfamily)
3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
c.25: Ferredoxin reductase-like, C-terminal NADP-linked domain [52342] (1 superfamily)
3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
c.26: Adenine nucleotide alpha hydrolase-like [52373] (3 superfamilies)
core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
c.27: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52417] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
c.28: Cryptochrome/photolyase, N-terminal domain [52424] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
c.31: DHS-like NAD/FAD-binding domain [52466] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-like
c.32: Tubulin nucleotide-binding domain-like [52489] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
c.33: Isochorismatase-like hydrolases [52498] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
c.34: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52506] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
c.39: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52732] (1 superfamily)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567
c.49: Pyruvate kinase C-terminal domain-like [52934] (2 superfamilies)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallel to the rest
c.55: Ribonuclease H-like motif [53066] (7 superfamilies)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
c.61: PRTase-like [53270] (1 superfamily)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
c.62: vWA-like [53299] (1 superfamily)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
c.65: Formyltransferase [53327] (1 superfamily)
3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest
c.66: S-adenosyl-L-methionine-dependent methyltransferases [53334] (1 superfamily)
core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
c.70: Nucleoside hydrolase [53589] (1 superfamily)
core: 3 layers, a/b/a ; mixed beta-sheet of 8 strands, order 32145687; strand 7 is antiparallel to the rest
c.82: ALDH-like [53719] (1 superfamily)
consists of two similar domains with 3 layers (a/b/a) each; duplication
core: parallel beta-sheet of 5 strands, order 32145
c.83: Aconitase iron-sulfur domain [53731] (1 superfamily)
consists of three similar domains with 3 layers (a/b/a) each; duplication
core: parallel beta-sheet of 5 strands, order 32145
c.86: Phosphoglycerate kinase [53747] (1 superfamily)
consists of two non-similar domains, 3 layers (a/b/a) each
Domain 1 has parallel beta-sheet of 6 strands, order 342156
Domain 2 has parallel beta-sheet of 6 strands, order 321456
c.87: UDP-Glycosyltransferase/glycogen phosphorylase [53755] (1 superfamily)
consists of two non-similar domains with 3 layers (a/b/a) each
domain 1: parallel beta-sheet of 7 strands, order 3214567
domain 2: parallel beta-sheet of 6 strands, order 321456
c.89: Phosphofructokinase [53783] (1 superfamily)
consists of two non-similar domains, 3 layers (a/b/a) each
Domain 1 has mixed sheet of 7 strands, order 3214567; strands 3 & 7 are antiparallel to the rest
Domain 2 has parallel sheet of 4 strands, order 2314
c.99: Dipeptide transport protein [63991] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; also contains a C-terminal alpha+beta subdomain
c.104: YjeF N-terminal domain-like [64152] (1 superfamily)
3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 32145678; strand 8 is antiparallel to the rest
c.107: DHH phosphoesterases [64181] (1 superfamily)
consists of two non-similar domains
Domain 1 has parallel sheet of 6 strands, order 321456
Domain 2 has mixed sheet of 5 strands, order 12345; strands 1 & 4 are antiparallel to the rest
c.108: HAD-like [56783] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
c.111: Activating enzymes of the ubiquitin-like proteins [69571] (1 superfamily)
3 layers: a/b/a; mixed beta-sheet of 8 strands, order 32145678; strands 6 and 8 are antiparallel to the rest
c.115: Hypothetical protein MTH777 (MT0777) [75180] (1 superfamily)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
c.118: GckA/TtuD-like [82543] (1 superfamily)
consists of two non-similar domains
Domain 1 has parallel sheet of 6 strands, order 321456, Rossmann-like topology
Domain 2 has mixed sheet of 6 strands, order 126345; strands 5 and 6 are antiparallel to the rest; some similarity to CbiF Domain 2
c.120: PIN domain-like [88722] (1 superfamily)
3 layers, a/b/a; core: parallel beta-sheet of 5 strands, order 32145
c.124: NagB/RpiA/CoA transferase-like [100949] (1 superfamily)
core: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456
c.134: LmbE-like [102587] (1 superfamily)
3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest; topological similarity to SAM-dependent methyltransferases
c.143: CofD-like [142337] (1 superfamily)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567; topological similarity to the CobT-like fold (52732)
d.106: SCP-like [55717] (1 superfamily)
alpha-beta(3)-(crossover)-beta-(alpha)-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 32145
d.283: Putative modulator of DNA gyrase, PmbA/TldD [111282] (1 superfamily)
consists of two different alpha+beta domains; d1: [duplication of alpha-beta(3)-alpha motif; 2 layers: a/b; antiparallel beta-sheet, order: 321456; strands 1, 2, 4 and 5 are twice longer than other secondary structures]; d2 [ complex fold; contains beta-barrel (n=5, S=10)]
d.351: NMB0488-like [160206] (1 superfamily)
duplication: two beta(3)-alpha motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456, shaped into a half-barrel; helical linker region
d.358: YdfO-like [160418] (1 superfamily)
duplication: two alpha(2)-beta(3) motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456
d.359: BH3703-like [160423] (1 superfamily)
alpha-beta(3)-alpha-beta(2)-alpha(2); antiparallel beta-sheet, order:32145; duplication: two alpha-beta(2) structural repeats are arranged with pseudo twofold symmetry
d.365: Ava3019-like [160531] (1 superfamily)
alpha(2)-beta-alpha-beta(4); 2 layers, a/b; antiparallel beta-sheet, order: 32145; similarity to the insert domain of Glucose 6-phosphate dehydrogenase-like family (sop_fa 55376)
e.50: AF1104-like [111320] (1 superfamily)
2 domains; d1: [all-alpha; 3-helical bundle, similar to the immunoglobulin/albumin-binding domain-like fold (46996)]; d2: [alpha/beta; 3 layers, a/b/a; 6-stranded mixed beta-sheet, order: 321456, strand 6 is antiparallel to the rest]
e.72: SSO1389-like [160979] (1 superfamily)
2 domains; d1: [alpha/beta, central parallel beta-sheet of 6 strands, order 321456, Rossmann-like]; d2: [alpha+beta, cluster of helices and a small 4-stranded beta-sheet]

Superfamily found:

c.72.3: CoaB-like [102645] (1 family)
combination of the Rossmann-like and Ribokinase-like topologies; mixed beta-sheet of 8 strands, order 32145678, strand 7 is antiparallel to the rest

Families found:

c.2.1.2: Tyrosine-dependent oxidoreductases [51751] (71 protein domains)
also known as short-chain dehydrogenases and SDR family
parallel beta-sheet is extended by 7th strand, order 3214567; left-handed crossover connection between strands 6 and 7
c.2.1.6: 6-phosphogluconate dehydrogenase-like, N-terminal domain [51868] (18 protein domains)
the beta-sheet is extended to 8 strands, order 32145678; strands 7 & 8 are antiparallel to the rest
C-terminal domains also show some similarity
c.52.1.26: Hypothetical protein VC1899 [117625] (1 protein)
contains 2 extra N-terminal domains; d1: [alpha/beta; 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest; topological similarity to the Formyltransferase fold (53327)]; d2: [distorted "winged helix" fold (46785)]
c.66.1.7: Protein-L-isoaspartyl O-methyltransferase [53354] (1 protein)
topological variant; strand order 3214567; strand 6 is antiparallel to the rest
c.120.1.2: 5' to 3' exonuclease catalytic domain [53045] (4 protein domains)
contains an alpha-helical arch and additional strand 6 antiparallel to the rest; strand order 321456; similarity to the resolvase-like fold

PDB Entry Domains found:

d1eloa2: 1elo A:5-282 [32145]
Elongation factor G (EF-G), N-terminal (G) domain (c.37.1.8) from Thermus thermophilus [TaxId:274]
Other proteins in same PDB: d1eloa1, d1eloa3, d1eloa4
d2eijf_: 2eij F: [132145]
Cytochrome c oxidase Subunit F (g.41.5.3) from Cow (Bos taurus) [TaxId:9913]
Other proteins in same PDB: d2eija_, d2eijb1, d2eijb2, d2eijc_, d2eijd_, d2eije_, d2eijg_, d2eijh_, d2eiji_, d2eijj_, d2eijk_, d2eijl_, d2eijm_, d2eijn_, d2eijo1, d2eijo2, d2eijp_, d2eijq_, d2eijr_, d2eijt_, d2eiju_, d2eijv_, d2eijw_, d2eijx_, d2eijy_, d2eijz_
automated match to d1occf_
complexed with cdl, chd, cu, cua, dmu, hea, mg, na, pek, pgv, psc, tgl, zn