- Serpins (56573)
contains a cluster of helices and a beta-sandwich
- FlhC-like (996536)
3 domains; d1 & d2 are similar three-helical bundles, with d1 containing an HTH motif; d3: zinc finger of a rubredoxin-like fold
- Api92-like (996530)
2 domains; d1: [alpha+beta with similarity to ferredoxin-like fold]; d2: [6 helices, bundle, one burid cebtral helix], inserted into d1
- PH0156-like (996524)
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]
- HI0933 insert domain-like (996518)
2 domains; d1: barrel, closed, n=6, S=12, greek-key; d2: four-helical bundle, inserted in d1
- SSO1389-like (996509)
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]
- MalF N-terminal region-like (996503)
consists of 3 N-terminal transmembrane helices, an alpha+beta linket domain and a beta-barrel (n=7; S=8) with one overside loop
- Flu NP-like (996497)
consists of alpha+beta and all-alpha domains; biological unit is a trimer
- CV3147-like (996491)
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]
- YacF-like (996485)
2 domains; d1: kinked four-helical bundle, inserted in d2: beta-sandwich of 7 strands in two sheets
- Viral glycoprotein ectodomain-like (996479)
complex fold; contains three rigid, mostly-beta domains and an alpha-helical region, acting as a conformatiomal switch ("fusion stalk")
- Poly(A) polymerase catalytic subunit-like (996469)
3 domains; d1: all-alpha, contains HhH motif; d2: alpha+beta of nucleotidyltransferase fold (scop_cf 81302); d3: [alpha+beta; beta(3)-alpha-beta(3)-alpha(2); 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 123654, strands 2 and 5 are antiparallel to the rest
- VPA0735-like (996463)
consists of a cluster of helices and two beta-sandwich domains of similar topology; probable duplication
- AF1531-like (996457)
2 domains; d1: incomplete barrel similar to the OB-fold domain of ribosomal L2 protein, d2: six helices, array
- FdhE-like (144019)
consists on the N-terminal five-helical bundle, a tandem repeat of two rubredoxin-like domains and the C-terminal helix packed together
- Replication terminator protein (Tus) (56595)
contains a cluster of helices and a beta-sandwich
- 2-methylcitrate dehydratase PrpD (103377)
consists of an all-alpha and alpha+beta domains
- Antivirulence factor (103382)
contains a helical bundle with a buried helix and an alpha+beta insert domain
- Virulence-associated V antigen (103387)
consists of an all-alpha and alpha+beta domains connected by antiparallel coiled coil
- Heme-dependent catalase-like (56633)
contains an (8,10) beta-barrel and an all-alpha domain
- Acyl-CoA dehydrogenase NM domain-like (56644)
2 domains: (1) all-alpha: 5 helices; (2) contains an open beta-sheet barrel: n*=5, S*=8; complex topology
- Carbohydrate phosphatase (56654)
N-terminal domain is an alpha+beta, C-terminal domain is an alpha/beta with mixed beta-sheet
- DNA/RNA polymerases (56671)
divided into morphological domains including "palm", "thumb" and "fingers"; the catalytic "palm" domain is conserved to all members
- beta and beta-prime subunits of DNA dependent RNA-polymerase (64483)
Multidomain subunits of complex domain organization
- Adenylylcyclase toxin (the edema factor) (81299)
3 domains: (1&2) alpha+beta, with domain 2 being inserted in domain 1; (3) all-alpha
- Prokaryotic type I DNA topoisomerase (56711)
4 domains: (1) Toprim alpha/beta; (2&4) "winged helix"-like; (3) barrel: n=6, S=8
- Type II DNA topoisomerase (56718)
4 domains: (1) toprim alpha/beta; (2) "winged helix"-like; (3) alpha+beta; (4) all-alpha
- DNA topoisomerase IV, alpha subunit (56725)
2 domains: (1) toprim alpha/beta; (2) "winged helix"-like
- DNA primase core (56730)
2 domains: (1) alpha+beta; (2) toprim alpha/beta
- Recombination protein RecR (111303)
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)
- Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment (56740)
2 domains: alpha+beta and all-beta
- D-aminoacid aminotransferase-like PLP-dependent enzymes (56751)
2 domains: (1) alpha+beta: beta3-alpha2-beta2; (2) alpha/beta, a part of its mixed sheet forms barrel: n=6, S=8
- HydB/Nqo4-like (56761)
3 domains: (1) all-alpha; (2&3) alpha+beta
- HydA/Nqo6-like (56769)
2 domains: (1) alpa/beta; (2) Fe-S cluster-bound
- Dehydroquinate synthase-like (56795)
2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array
- Siroheme synthase middle domains-like (75614)
2 domains: (1) alpha+beta, 2 layers; (2) 3/4-helical bundle, right-handed twist, left-handed superhelix
- Acetyl-CoA synthetase-like (56800)
4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta
- Ribosomal protein L1 (56807)
2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
- Release factor (75619)
4 domains: (1) 3-helical bundle; (2) alpha+beta of ferredoxin-like fold (3 and 4) alpha+beta of dsRDB-like fold
- YaeB-like (118195)
2 domains; d1: [beta-barrel (n=6, S=10), similar to the Reductase/isomerase/elongation factor common domain fold (scop_cf 50412), provides homodimerisation interface]; d2: [alpha+beta (disordered)]
- YebC-like (75624)
3 domains: (1) 3-helical bundle; (2 and 3 ) alpha+beta of different folds: domain 3 has a ferredoxin-like fold and is inserted in domain 2
- Cullin homology domain (75631)
3 domains: (1) 4-helical bundle; (2) alpha+beta; (3) "winged helix"-like
- Sec1/munc18-like (SM) proteins (56814)
3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2
- Prismane protein-like (56820)
3 domains: (1) spectrin repeat-like 3-helical bundle; (2 and 3) alpha/beta: Rossmann-fold topology
- Subunits of heterodimeric actin filament capping protein Capz (90095)
3 domains: (1) protozoan pheromone-like alpha-helical bundle; (2) rubredoxin-like domain lacking metal-binding site; (3) alpha+beta heterodimerisation domain: alpha-beta(5)-alpha
- beta-lactamase/transpeptidase-like (56600)
contains a cluster of helices and an alpha+beta sandwich
- Upper collar protein gp10 (connector protein) (56825)
2 domains: (1) alpha-helical bundle; (2) beta-barrel (n=5, S=8)
- Phase 1 flagellin (64517)
3 domains: (1) alpha-helical bundle; (2&3) complex all-beta folds
- 39 kda initiator binding protein, IBP39, C-terminal domains (103408)
2 closely associated domains: (1) all-alpha, EF-hand like; (2) alpha+beta, Frataxin-like
- AF1104-like (111320)
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]
- Urocanase (111325)
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
- NAD kinase/diacylglycerol kinase-like (111330)
2 domains: d1 [alpha/beta; related to the PFK N-terminal domain (scop_sf 53784)]; d2 [all-beta; atypical beta-sandwich made of 4 structural repeats of beta(3) unit]
- QueA-like (111336)
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)
- CbiD-like (111341)
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
- Rap/Ran-GAP (111346)
consists of two domains; d1: alpha+beta (78-190; alpha-beta(4)-alpha-beta-alpha; 3 layers; antiparallel beta-sheet of 5 strands; order 51234); d2: alpha/beta similar to the G-domain fold (191-381; scop_fa 52592)
- Vacuolar ATP synthase subunit C (118202)
2 alpha+beta (sub)domains [each has a ferredoxin-like fold; scop_cf 54861], connected with 3-helical bundle; duplication: two repeats of beta-alpha-beta-[alpha coiled-coil]-beta-alpha-beta motif
- Thermophilic metalloprotease-like (144051)
consists of two domains; d1: alpha/beta (3 layers, a/b/a; parralel beta-sheet, order 2134); d2: pseudo beta-barrel capped by helices
- ImpE-like (144058)
consists of two domains; d1: right-handed superhelix of five helices; d2: pseudo beta-barrel containing structurally similar part to the "Histone-like" proteins from archaea (scop_fa 54161)
- Heme iron utilization protein-like (144063)
2 domains; d1 - 3-helical bundle similar to the homeodomain-like fold; d2 - 6-stranded beta-barrel capped by two helices at one end, similar topology to the PH-like fold
- NSP3 homodimer (69902)
2 domains: (1) all-alpha, (2) alpha+beta; asymmetric homodimer with each domain intertwining with its counterpart
- E2F-DP heterodimerization region (144073)
heterodimeric fold with the N-terminal long helices of both chains forming a parallel coiled coil and their C-terminal folded beta-hairpins interlocking together in a beta-sandwich
- Membrane penetration protein mu1 (69907)
4 domains: three intertwined predominately alpha domains and one jelly-roll beta-sandwich
- Reovirus inner layer core protein p3 (56830)
large protein without apparent domain division; has a number of all-alpha regions and one all beta domain near the C-end
- L-A virus major coat protein (82855)
large protein without apparent domain division
- Major capsid protein VP5 (103416)
large protein without apparent domain division
- Viral ssDNA binding protein (118207)
2 domains; d1: [large alpha+beta domain subdivided into the 'head', 'neck' and 'shoulders' regions; in the 'neck', there is an OB-fold interrupted by large insertions]; d2: [all-alpha, 6 helices; orthogonal array]