| SCOP superfamily ID |
superfamiily description |
corresponding fold description |
| c.2.1 | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains 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.88.1 | Glutaminase/Asparaginase | Glutaminase/Asparaginase consists of two non-similar alpha/beta domains, 3 layers (a/b/a) each ! Domain 1 has mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest; left-handed crossover connection between strands 4 and 5 ! Domain 2 has parallel beta-sheet of 4 strands, order 1234 |
| c.130.1 | Alpha-2,3/8-sialyltransferase CstII | Alpha-2,3/8-sialyltransferase CstII 3 layers: a/b/a; parallel beta-sheet of 8 strands, order 54321678 |
| c.82.1 | ALDH-like binds NAD differently from other NAD(P)-dependent oxidoreductases ! | ALDH-like consists of two similar domains with 3 layers (a/b/a) each; duplication ! core: parallel beta-sheet of 5 strands, order 32145 |
| c.72.1 | Ribokinase-like has extra strand located between strands 2 and 3 ! | Ribokinase-like core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest ! potential superfamily: members of this fold have similar functions but different ATP-binding sites |
| d.159.1 | Metallo-dependent phosphatases different families of this superfamily are groupped in a single Pfam family, | Metallo-dependent phosphatases 4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication |
| c.135.1 | NIF3 (NGG1p interacting factor 3)-like di-iron binding protein ! | NIF3 (NGG1p interacting factor 3)-like consist of two intertwined domains; duplication: contains two structural repeats of alpha-beta-(beta-alpha)3 motif with mixed beta-sheet, order: 1432, strand 1 is antiparallel to the rest |
| c.1.9 | Metallo-dependent hydrolases the beta-sheet barrel is similarly distorted and capped by a C-terminal helix ! has transition metal ions bound inside the barrel ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.87.1 | UDP-Glycosyltransferase/glycogen phosphorylase | UDP-Glycosyltransferase/glycogen phosphorylase 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.37.1 | P-loop containing nucleoside triphosphate hydrolases division into families based on beta-sheet topologies ! | P-loop containing nucleoside triphosphate hydrolases 3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes |
| c.52.3 | Eukaryotic RPB5 N-terminal domain | Restriction endonuclease-like core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest |
| c.93.1 | Periplasmic binding protein-like I Similar in architecture to the superfamily II but partly differs in topology ! | Periplasmic binding protein-like I consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication ! parallel beta-sheet of 6 strands, order 213456 |
| c.8.2 | LeuD/IlvD-like contains mixed beta-sheet barrel, closed n=7, S=10 ! | The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it |
| c.70.1 | Nucleoside hydrolase | Nucleoside hydrolase core: 3 layers, a/b/a ; mixed beta-sheet of 8 strands, order 32145687; strand 7 is antiparallel to the rest |
| c.111.1 | Activating enzymes of the ubiquitin-like proteins transfer adenylyl group to the C-terminal carboxyl group of the ubiquitin and MoaD/ThiS-related proteins ! the ATP nucleotide-binding site is similar to that of the NAD-binding Rossmann-folds ! | Activating enzymes of the ubiquitin-like proteins 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 32145678; strands 6 and 8 are antiparallel to the rest |
| c.86.1 | Phosphoglycerate kinase | Phosphoglycerate kinase 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.41.1 | Subtilisin-like | Subtilisin-like 3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3 |
| c.23.1 | CheY-like | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.1.15 | Xylose isomerase-like different families share similar but non-identical metal-binding sites ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.73.1 | Carbamate kinase-like the sheet topology is similar to those of undecaprenyl diphosphate synthase and the N-terminal domain of phosphoglycerate kinase ! | Carbamate kinase-like 3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786; strand 8 is antiparallel to the rest |
| c.68.1 | Nucleotide-diphospho-sugar transferases | Nucleotide-diphospho-sugar transferases 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest |
| c.3.1 | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander |
| c.1.10 | Aldolase Common fold covers whole protein structure ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.26.2 | Adenine nucleotide alpha hydrolases-like share similar mode of ligand (Adenosine group) binding ! can be subdivided into two group with closer relationships within each group than between the groups; the first three families form one group whereas the last two families form the other group ! | Adenine nucleotide alpha hydrolase-like core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145 |
| c.66.1 | S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest |
| c.24.1 | Methylglyoxal synthase-like contains a common phosphate-binding site ! | Methylglyoxal synthase-like 3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145 |
| c.23.11 | Beta-D-glucan exohydrolase, C-terminal domain | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.92.2 | "Helical backbone" metal receptor contains a long alpha helical insertion in the interdomain linker ! | Chelatase-like duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134 |
| c.9.1 | Barstar-related | Barstar-like 2 layers, a/b; parallel beta-sheet of 3 strands, order 123 |
| c.129.1 | MCP/YpsA-like | MCP/YpsA-like 3 layers: a/b/a, parallel beta-sheet of 7 strands, order 4321567 |
| c.23.13 | Type II 3-dehydroquinate dehydratase | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.13.2 | SpoIIaa-like | SpoIIaa-like core: 4 turns of a (beta-alpha)n superhelix |
| c.114.1 | DsrEFH-like | DsrEFH-like 3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 43215 |
| c.42.1 | Arginase/deacetylase | Arginase/deacetylase 3 layers: a/b/a, parallel beta-sheet of 8 strands, order 21387456 |
| c.23.10 | SGNH hydrolase | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.14.1 | ClpP/crotonase | ClpP/crotonase core: 4 turns of (beta-beta-alpha)n superhelix |
| e.49.1 | Recombination protein RecR | Recombination protein RecR consists of three domains: alpha-helical dimerisation domain (res. 1-53) with HhH motif; 'treble cleft' C4 zinc-finger domain (54-76); and Toprim domain (76-199; segment-swapped dimer) |
| c.53.1 | Resolvase-like | Resolvase-like Core: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest |
| e.19.1 | HydA/Nqo6-like | HydA/Nqo6-like 2 domains: (1) alpa/beta; (2) Fe-S cluster-bound |
| c.1.16 | Bacterial luciferase-like consists of clearly related families of somewhat different folds ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.98.2 | HprK N-terminal domain-like probable phosphatase ! | MurF and HprK N-domain-like core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1234; structural similarity of the MurF and HprK extends beyond the core. |
| c.10.1 | RNI-like regular structure consisting of similar repeats ! | Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) 2 curved layers, a/b; parallel beta-sheet; order 1234...N; there are sequence similarities between different superfamilies |
| c.79.1 | Tryptophan synthase beta subunit-like PLP-dependent enzymes | Tryptophan synthase beta subunit-like PLP-dependent enzymes consists of two similar domains related by pseudo dyad; duplication ! core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214 |
| c.7.1 | PFL-like glycyl radical enzymes duplication: the N- and C-terminal halves have similar topologies ! | PFL-like glycyl radical enzymes contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel |
| c.8.5 | GroEL apical domain-like | The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it |
| c.40.1 | Methylesterase CheB, C-terminal domain | Methylesterase CheB, C-terminal domain 3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3421567 |
| c.23.16 | Class I glutamine amidotransferase-like conserved positions of the oxyanion hole and catalytic nucleophile; different constituent families contain different additional structures ! | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.67.1 | PLP-dependent transferases | PLP-dependent transferase-like main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest |
| d.157.1 | Metallo-hydrolase/oxidoreductase | Metallo-hydrolase/oxidoreductase duplication of beta(4)-alpha-beta-alpha motif; 4 layers a/b/b/a; mixed beta-sheets |
| c.1.21 | Dihydropteroate synthetase-like | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.1.6 | PLP-binding barrel circular permutation of the canonical fold: begins with an alpha helix and ends with a beta-strand ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.5.1 | MurCD N-terminal domain | MurCD N-terminal domain 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group |
| c.1.31 | ThiG-like shares the common phosphate-binding site with other superfamilies ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.72.3 | CoaB-like combination of the Rossmann-like and Ribokinase-like topologies; mixed beta-sheet of 8 strands, order 32145678, strand 7 is antiparallel to the rest ! | Ribokinase-like core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest ! potential superfamily: members of this fold have similar functions but different ATP-binding sites |
| c.25.1 | Ferredoxin reductase-like, C-terminal NADP-linked domain binds NADP differently than classical Rossmann-fold ! N-terminal FAD-linked domain contains (6,10) barrel ! | Ferredoxin reductase-like, C-terminal NADP-linked domain 3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145 |
| c.1.17 | Nicotinate/Quinolinate PRTase C-terminal domain-like incomplete beta/alpha barrel with parallel beta-sheet of 7 strands ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.78.1 | Aspartate/ornithine carbamoyltransferase | ATC-like consists of two similar domains related by pseudo dyad; duplication ! core: 3 layers, a/b/a, parallel beta-sheet of 4 strands, order 2134 |
| c.1.12 | Phosphoenolpyruvate/pyruvate domain | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.23.4 | Succinyl-CoA synthetase domains | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.1.2 | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.72.2 | MurD-like peptide ligases, catalytic domain has extra strand located between strands 1 and 2 ! | Ribokinase-like core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest ! potential superfamily: members of this fold have similar functions but different ATP-binding sites |
| c.23.14 | N-(deoxy)ribosyltransferase-like there are similar active site architectures as well as the catalytic mechanisms of functionally characterised members ! | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.17.1 | Caspase-like mature protein may be composed of two chains folded in a single domain ! | Caspase-like 3 layers, a/b/a; core: mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest |
| c.102.1 | Cell-division inhibitor MinC, N-terminal domain | Cell-division inhibitor MinC, N-terminal domain beta(2)-(alpha-beta)2-beta; 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 1 & 5 are antiparallel to the rest |
| c.36.1 | Thiamin diphosphate-binding fold (THDP-binding) there are two different functional modules of this fold: pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules ! two Pyr and two PP modules assemble together in a conserved heterotetrameric core that binds two THDP coenzyme molecules ! | Thiamin diphosphate-binding fold (THDP-binding) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465 |
| c.18.1 | Uracil-DNA glycosylase-like | Uracil-DNA glycosylase-like 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134 |
| c.23.12 | Formate/glycerate dehydrogenase catalytic domain-like | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| e.26.1 | Prismane protein-like | Prismane protein-like 3 domains: (1) spectrin repeat-like 3-helical bundle; (2 and 3) alpha/beta: Rossmann-fold topology |
| c.81.1 | Formate dehydrogenase/DMSO reductase, domains 1-3 molybdopterine enzyme ! | Formate dehydrogenase/DMSO reductase, domains 1-3 contains of two similar intertwined domains related by pseudo dyad; duplication ! core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451 |
| c.1.33 | EAL domain-like variant of the beta/alpha-barrel fold with strand 1 being antiparallel to the rest ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.1.8 | (Trans)glycosidases | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.80.1 | SIS domain | SIS domain 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345 |
| c.1.24 | Pyridoxine 5'-phosphate synthase | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.1.5 | Inosine monophosphate dehydrogenase (IMPDH) The phosphate moiety of substrate binds in the 'common' phosphate-binding site ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.1.11 | Enolase C-terminal domain-like binds metal ion (magnesium or manganese) in conserved site inside barrel ! N-terminal alpha+beta domain is common to this superfamily ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.23.6 | Cobalamin (vitamin B12)-binding domain | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.57.1 | Molybdenum cofactor biosynthesis proteins | Molybdenum cofactor biosynthesis proteins 3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallel to the rest; permutation of the Phosphorylase/hydrolase-like fold |
| c.77.1 | Isocitrate/Isopropylmalate dehydrogenase-like the constituent families form similar dimers ! | Isocitrate/Isopropylmalate dehydrogenase-like consists of two intertwined (sub)domains related by pseudo dyad; duplication ! 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest |
| c.33.1 | Isochorismatase-like hydrolases | Isochorismatase-like hydrolases 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456 |
| c.1.22 | UROD/MetE-like | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.69.1 | alpha/beta-Hydrolases many members have left-handed crossover connection between strand 8 and additional strand 9 ! | alpha/beta-Hydrolases core: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 is antiparallel to the rest |
| c.1.4 | FMN-linked oxidoreductases | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.119.1 | DAK1/DegV-like domain folds and architecture show some similarity to the tubulin-like GTPases; the nucleotide-binding sites of the Dihydroxyacetone kinase and tubulin families are different ! | DAK1/DegV-like 2 different domains; d1: [core: 3 layers, a/b/a; parallel sheet of 5 strands, order: 2134]; D2: [2 layers, a/b; mixed sheet of 6 strands, order 321645; strands 2 and 6 are antiparallel to the rest] |
| c.28.1 | Cryptochrome/photolyase, N-terminal domain | Cryptochrome/photolyase, N-terminal domain 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like |
| c.49.1 | PK C-terminal domain-like | Pyruvate kinase C-terminal domain-like 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallel to the rest |
| c.23.17 | Precorrin-8X methylmutase CbiC/CobH fold elaborated with additional structures ! | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.1.18 | PLC-like phosphodiesterases | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.46.1 | Rhodanese/Cell cycle control phosphatase | Rhodanese/Cell cycle control phosphatase 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451 |
| c.55.5 | Nitrogenase accessory factor-like | Ribonuclease H-like motif 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest |
| c.104.1 | YjeF N-terminal domain-like possible circular permutation of the ribokinase-like fold (of the YjeF C-terminal domain) ! | YjeF N-terminal domain-like 3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 32145678; strand 8 is antiparallel to the rest |
| c.1.23 | FAD-linked oxidoreductase distinct cofactor-binding mode from both FMN- and NAD(P)-linked TIM-barrel oxidoreductases; families are related by a circular permutation ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.89.1 | Phosphofructokinase | Phosphofructokinase 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.65.1 | Formyltransferase | Formyltransferase 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest |
| c.1.26 | Homocysteine S-methyltransferase | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.56.5 | Zn-dependent exopeptidases core: mixed beta-sheet of 8 strands, order 12435867; strands 2, 6 & 7 are antiparallel to the rest ! | Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops |
| c.145.1 | NadA-like | NadA-like duplication; consists of three similar domains related by pseudo threefold symmetry; 3 layers, a/b/a; parallel beta sheet, order: 2134 |
| e.23.1 | Acetyl-CoA synthetase-like | Acetyl-CoA synthetase-like 4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta |
| c.124.1 | NagB/RpiA/CoA transferase-like | NagB/RpiA/CoA transferase-like core: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456 |
| c.134.1 | LmbE-like | LmbE-like 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.127.1 | F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) the sheet topology is similar to those of the Periplasmic binding protein-like I domains ! | F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213456 |
| c.1.30 | CutC-like | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.4.1 | Nucleotide-binding domain this superfamily shares the common nucleotide-binding site with and provides a link between the Rossmann-fold NAD(P)-binding and FAD/NAD(P)-binding domains ! | Nucleotide-binding domain 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like |
| c.1.3 | Thiamin phosphate synthase | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.56.7 | AF0625-like contains extra C-terminal alpha/beta domain: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134 ! | Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops |
| c.8.7 | RraA-like structural similarity and possible distant homology to the phosphohistidine domain of pyruvate phosphate dikinase ! | The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it |
| c.54.1 | PTS system fructose IIA component-like active dimer is formed by strand 5 swapping ! | PTS system fructose IIA component-like 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest |
| c.23.5 | Flavoproteins | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.55.1 | Actin-like ATPase domain duplication contains two domains of this fold ! | Ribonuclease H-like motif 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest |
| c.55.3 | Ribonuclease H-like consists of one domain of this fold ! | Ribonuclease H-like motif 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest |
| c.1.28 | Radical SAM enzymes common Fe-S cluster and SAM binding sites are embedded into complete or incomplete beta/alpha-barrel ! | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.108.1 | HAD-like usually contains an insertion (sub)domain after strand 1 ! | HAD-like 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456 |
| c.8.1 | Phosphohistidine domain contains barrel, closed, n=7, S=10 ! | The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it |
| c.1.14 | RuBisCo, C-terminal domain | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.8.10 | LD-carboxypeptidase A C-terminal domain-like | The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it |
| c.21.1 | Ribosomal protein L13 | Ribosomal protein L13 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 3214 |
| c.44.2 | PTS system IIB component-like | Phosphotyrosine protein phosphatases I-like 3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134 |
| c.38.1 | PTS IIb component | PTS IIb component 3 layers: a/b/a, parallel beta-sheet of 6 strands, order 324156 |
| c.61.1 | PRTase-like | PRTase-like core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest |
| c.1.1 | Triosephosphate isomerase (TIM) | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.1.19 | Cobalamin (vitamin B12)-dependent enzymes | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.146.1 | YgbK-like | YgbK-like consists of two domains with partial topological similarity to the P-loop kinases but without the P-loop motif; the domain association results in the formation of a single mixed beta-sheet of 15 strands |
| c.26.1 | Nucleotidylyl transferase | Adenine nucleotide alpha hydrolase-like core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145 |
| e.51.1 | Urocanase | Urocanase 3 domains; d1: alpha+beta [alpha(2)-beta(3); mixed sheet: 213]; d2: alpha/beta of the NAD(P)-binding Rossmann-fold superfamily (scop_sf 51735, most similar to scop_fa 51883 and scop_fa 51736); d3: alpha+beta of the glutamine synthetase/guanido kinase fold (scop_cf 55930); d1 and d3 form a single beta-sheet |
| c.8.6 | Swiveling domain of dehydratase reactivase alpha subunit | The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it |
| c.143.1 | CofD-like | CofD-like 3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567; topological similarity to the CobT-like fold (scop_cf 52732) |
| c.62.1 | vWA-like | vWA-like core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest |
| e.22.1 | Dehydroquinate synthase-like | Dehydroquinate synthase-like 2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array |
| c.153.1 | YerB-like | YerB-like 3 layers: b/b/a; central mixed beta-sheet of 9 strands, order 541329678; strands 3 and 7 are antiparallel to the rest; an unusual "over the other end" connection between strands 3 and 4 |
| c.118.1 | GckA/TtuD-like | GckA/TtuD-like 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 |
| e.25.1 | Sec1/munc18-like (SM) proteins | Sec1/munc18-like (SM) proteins 3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2 |
| c.115.1 | Hypothetical protein MTH777 (MT0777) | Hypothetical protein MTH777 (MT0777) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456 |
| c.113.1 | HemD-like | HemD-like duplication: consists of two similar 'swapped' domain with 3 layers (a/b/a) each; parallel beta-sheet of 5 strands, order 21345 |
| c.92.3 | PrpR receptor domain-like recent PDB entry 2q5c belongs to this superfamily | Chelatase-like duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134 |
| c.59.1 | MurD-like peptide ligases, peptide-binding domain | MurD-like peptide ligases, peptide-binding domain 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 is antiparallel to the rest |
| c.6.3 | PHP domain-like | 7-stranded beta/alpha barrel variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567; some members may have fewer strands |
| c.92.1 | Chelatase interdomain linker is short; swapping of C-terminal helices between the two domains ! | Chelatase-like duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134 |
| c.83.1 | Aconitase iron-sulfur domain | Aconitase iron-sulfur domain consists of three similar domains with 3 layers (a/b/a) each; duplication ! core: parallel beta-sheet of 5 strands, order 32145 |
| c.23.8 | N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| e.50.1 | AF1104-like | AF1104-like 2 domains; d1: [all-alpha; 3-helical bundle, similar to the immunoglobulin/albumin-binding domain-like fold (scop_cf 46996)]; d2: [alpha/beta; 3 layers, a/b/a; 6-stranded mixed beta-sheet, order: 321456, strand 6 is antiparallel to the rest] |
| c.23.3 | Hypothetical protein MTH538 | Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 |
| c.34.1 | Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | Homo-oligomeric flavin-containing Cys decarboxylases, HFCD 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456 |
| c.1.7 | NAD(P)-linked oxidoreductase | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.1.20 | tRNA-guanine transglycosylase | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.32.1 | Tubulin nucleotide-binding domain-like | Tubulin nucleotide-binding domain-like 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456 |
| c.26.3 | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | Adenine nucleotide alpha hydrolase-like core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145 |
| c.1.29 | GlpP-like | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.123.1 | CoA-transferase family III (CaiB/BaiF) | CoA-transferase family III (CaiB/BaiF) consist of two different alpha/beta domains; N-terminal domain has a SurE-like topology with a left-handed beta-alpha-beta unit |
| c.19.1 | FabD/lysophospholipase-like | FabD/lysophospholipase-like core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 is antiparallel to the rest |
| c.138.1 | Indigoidine synthase A-like | Indigoidine synthase A-like core: 3 layers, a/b/a; parallel beta-sheet of 7 strands, order 2134756 |
| c.27.1 | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like |
| c.101.1 | Undecaprenyl diphosphate synthase the sheet topology is similar to those of the N-terminal domain of phosphoglycerate kinase and carbamate kinase ! | Undecaprenyl diphosphate synthase 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 342156 |
| c.56.2 | Purine and uridine phosphorylases complex architecture; contains mixed beta-sheet of 8 strands, order 23415867, strands 3, 6 & 7 are antiparallel to the rest; and barrel, closed; n=5, S=8 ! | Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops |
| c.50.1 | Macro domain-like | Macro domain-like 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 165243, strand 3 is antiparallel to the rest |
| c.105.1 | 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain | 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 45321678, strands 4 and 5 are antiparallel to the rest |
| c.67.2 | PhnH-like single domain protein of similar topology to the core domain of PLP-transferases | PLP-dependent transferase-like main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest |
| e.60.1 | Thermophilic metalloprotease-like | Thermophilic metalloprotease-like consists of two domains; d1: alpha/beta (3 layers, a/b/a; parralel beta-sheet, order 2134); d2: pseudo beta-barrel capped by helices |
| c.151.1 | CobE/GbiG C-terminal domain-like probably involved in deacylation steps in both anaerobic and aerobic pathways of cobalamin biosynthesis | CobE/GbiG C-terminal domain-like 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32154; strand 5 is antiparallel to the rest |
| c.16.1 | Lumazine synthase | Lumazine synthase 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134 |
| c.39.1 | Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) | Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) 3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567 |
| c.1.13 | Malate synthase G | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.121.1 | Ribose/Galactose isomerase RpiB/AlsB | Ribose/Galactose isomerase RpiB/AlsB 3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 21354; topological similarity to a part of the arginase/deacetylase fold |
| c.76.1 | Alkaline phosphatase-like | Alkaline phosphatase-like core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 is antiparallel to the rest |
| c.1.27 | (2r)-phospho-3-sulfolactate synthase ComA | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.20.1 | Initiation factor IF2/eIF5b, domain 3 | Initiation factor IF2/eIF5b, domain 3 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134 |
| c.8.8 | Putative cyclase contains mixed beta-sheet barrel, closed n=7, S=10 ! | The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it |
| c.8.4 | PA domain | The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it |
| c.56.4 | Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) | Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops |
| d.160.1 | Carbon-nitrogen hydrolase | Carbon-nitrogen hydrolase 4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication |
| c.6.1 | Glycosyl hydrolases family 6, cellulases | 7-stranded beta/alpha barrel variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567; some members may have fewer strands |
| c.100.1 | Thiamin pyrophosphokinase, catalytic domain | Thiamin pyrophosphokinase, catalytic domain 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 432156 |
| c.10.3 | Outer arm dynein light chain 1 (beta-beta-alpha)n superhelix ! | Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) 2 curved layers, a/b; parallel beta-sheet; order 1234...N; there are sequence similarities between different superfamilies |
| c.110.1 | DTD-like active form is a dimer ! | DTD-like beta(2)-(alpha-beta)2-beta(3); 3 layers, a/b/b; some topological similarity to the N-terminal domain of MinC |
| c.8.9 | FumA C-terminal domain-like | The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it |
| e.67.1 | PH0156-like | PH0156-like 2 (sub)domains; d1: [alpha/beta with central mixed beta-sheet, order: 23415876, similarity to the G protein but no P-loop]; d2: [all-alpha, 5 helices, provides dimerization interface] |
| c.55.2 | Creatinase/prolidase N-terminal domain | Ribonuclease H-like motif 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest |
| c.144.1 | RibA-like | RibA-like 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 1235467, strands 1 and 3 are antiparallel to the rest; partial topological similarity to some alpha/beta hydrolases (scop_cf 53473) |
| c.106.1 | SurE-like some topological similarity to the N-terminal domain of Glutaminase/Asparaginase family ! | SurE-like 3 layers: a/b/a; mixed beta-sheet of 9 strands, order 342156798; strands 3, 8 and 9 are antiparallel to the rest; left-handed crossover connection between strands 6 and 7 |
| c.56.3 | Peptidyl-tRNA hydrolase-like | Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops |
| e.10.1 | Prokaryotic type I DNA topoisomerase duplication: the protein chain passing through the domains 2-4 makes two structural repeats ! The active site is formed by the toprim and "winged helix" domains (domains 1 and 4); these two domains are also found in the type II topoisomerase (DNA gyrase A) and in the alpha subunit of topoisomerase IV ! | Prokaryotic type I DNA topoisomerase 4 domains: (1) Toprim alpha/beta; (2&4) "winged helix"-like; (3) barrel: n=6, S=8 |
| c.125.1 | Creatininase | Creatininase 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134 |
| e.13.1 | DNA primase core | DNA primase core 2 domains: (1) alpha+beta; (2) toprim alpha/beta |
| c.85.1 | FucI/AraA N-terminal and middle domains | FucI/AraA N-terminal and middle domains consists of two domains of similar topology, 3 layers (a/b/a) each ! Domain 1 (1-173) has parallel beta-sheet of 5 strands, order 21345 ! Domain 2 (174-355) has parallel beta-sheet of 4 strands, order 2134 |
| e.72.1 | SSO1389-like | SSO1389-like 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] |
| e.54.1 | CbiD-like | CbiD-like 2 domains; (1) alpha+beta (res 1-192), a circularly permuted rS5 domain 2-like fold (scop_cf 54210); (2) alpha/beta with parallel beta-sheet of 4 strands, order 2134 |
| c.56.1 | HybD-like the HybD fold coincides with the consensus core structure ! | Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops |
| c.96.1 | Fe-only hydrogenase | Fe-only hydrogenase consist of two intertwined domains; contains partial duplication |
| c.147.1 | CAC2185-like | CAC2185-like consists of two non-similar domains, 3 layers (a/b/a) each; d1 has parallel sheet of 4 strands, order 2134; d2 has parallel sheet of 5 strands, order 21345, and antiparallel meander sheet of 3 strands |
| c.99.1 | Dipeptide transport protein | Dipeptide transport protein 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; also contains a C-terminal alpha+beta subdomain |
| c.142.1 | Nqo1 FMN-binding domain-like | Nqo1 FMN-binding domain-like 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214 |
| c.141.1 | Glycerate kinase I | Glycerate kinase I consists of two different alpha/beta domains; (1) of the Flavodoxin-like fold (scop_cf 52171); (2) similar to the Restriction endonuclease-like fold (scop_cf 52979), inserted into domain 1 |
| c.1.25 | Monomethylamine methyltransferase MtmB | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| c.53.2 | beta-carbonic anhydrase, cab | Resolvase-like Core: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest |
| c.56.8 | Cgl1923-like | Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops |
| c.1.32 | TM1631-like | TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites |
| e.53.1 | QueA-like | QueA-like 2 domains; d1 (1-64,174-335) [alpha/beta; 3 layers, a/b/a; mixed beta sheet of 9 strands, order: 219863457; strands 1, 5 and 8 are antiparallel to the rest]; d2 (65-142) [all-beta; barrel, closed (n=6, S=10); greek-key; topologically similar to the split barrel fold (scop_cf 50474) |
| e.73.1 | CV3147-like | CV3147-like 2 domains; d1: [alpha/beta; 3 layers, a/b/a, mixed beta-sheet of 8 strands, order 12543876, strands 1, 7 and 8 are antiparallel to the rest]; d2: [pseudo beta-barrel of 6 strands, meander] |