Cysteine proteinases [54000] (1)
consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
Cysteine proteinases [54001] (16) the constitute families differ by insertion into and circular permutation of the common catalytic core made of one alpha-helix and 3-strands of beta-sheet
His-Me finger endonucleases [54059] (1)
core: (alpha)-beta-omega_loop-beta-alpha; embeded in larger different structures
His-Me finger endonucleases [54060] (6) common motif contains conserved histidine residue and metal-binding site
RNase A-like [54075] (1)
contains long curved beta-sheet and 3 helices
RNase A-like [54076] (1) can be classified as disulfide-rich
EndoU-like [142876] (1)
comprises several helices and two three-stranded antiparallel beta-sheets; similar architecture to the RNase A-like fold (scop_cf 54075)
EndoU-like [142877] (2) similarity to the RNase A-like superfamily (scop_sf 54076) extends to the active site location and architecture; the two structural cores of the RNase A and EndoU superfamilies are interrelated by a topological permutation - transposition of two pereferial beta-strands, suggesting possible distant homology of the two superfamilies (and their unification in a hyperfamily)
PhtA domain-like [142887] (1) contains extra N-terminal beta-hairpin, like structurally similar archaeal "histone-like" proteins (scop_fa 54161), but does not adopt its SH3-like barrel fold
Ribosome binding domain-like [100965] (2)
beta-(2)-alpha(2)-beta(2); 2 layers: beta/alpha; antiparallel beta-sheet: order 1243; topological similarity to the common core of ribosomal proteins L23 and L15e
Obg GTP-binding protein C-terminal domain [102740] (1)
beta-(2)-alpha(3)-beta(2); 2 layers: beta/alpha; mixed beta-sheet: order 1234; strands 2 and 3 a parallel to each other
YjbR-like [142906] (1) overall similar to the Type III secretory system chaperone subunits; different shape of the beta-sheet
DNA-binding domain of intron-encoded endonucleases [64495] (1)
beta(2)-alpha(2)-beta; 2 layers; 3-stranded antiparallel beta-sheet, order 213; HTH motif; also includes the extra N-terminal, DNA minor groove-binding helix
WGR domain-like [142920] (1)
beta(4)-alpha-X-beta; 2 layers, a/b; antiparallel beta-sheet, order 51234; the beta-hairpin insetrion in strand 1 results in the formation of a beta-triangle structure
Putative dsDNA mimic [102816] (1) elaborated with additional structures; some similarity to Uracil-DNA glycosylase (UGI) and Nuclease A (NuiA) inhibitors
Pre-PUA domain [88802] (4) this domain is found in association with the PUA domain in the C-terminal region of Archaeosine tRNA-guanine transglycosylase and related stand-alone proteins
Nuclease A inhibitor (NuiA) [82602] (1) some structural similarity to Uracil-DNA glycosylase inhibitor and putative dsDNA mimic HI1450 of the cystatin-like fold
Kinetochore globular domain [143026] (2) swapped heterodimer with the N-terminal helices; Spc24-like subunits have the core fold, whereas Spc25-like subunits have a variant fold
Photosystem I subunit PsaD [64233] (1)
beta-BETA(2)-beta-alpha-beta(2); antiparallel sheet: order 2134 packed against helix and BETA-hairpin on the same side; irregular C-terminal tail
TTHA1013-like [143099] (1)
beta(3)-alpha-beta; 2 layers; mixed beta-sheet, order 4123, strands 1 and 4 are parallel to each other; topological similarity to the SEP domain fold (scop_cf 102847); dimerises via the long C-terminal strand with the formation of a single beta-sheet
YefM-like [143119] (1)
core: beta-alpha(2)-beta(2)-alpha; mixed beta-sheet, order:123, strands 1 and 2 are parallel; forms compact dimer with a single beta-sheet;
VSV matrix protein [75403] (1)
beta-alpha(2)-beta(4)-alpha-beta(2); two layers: alpha/beta; bifurcated coiled beta-sheet: order of the first 5 strands: 23154
DNA-binding domain of Mlu1-box binding protein MBP1 [54616] (1) has some topological similarity to the "winged helix" DNA-binding domain, to B1 and B5 domains of PheRS-beta (1PYS CH B) and to methyl-CpG-binding domain
Hypothetical protein Ta1206 [102890] (1)
beta(4)-alpha-beta(2)-alpha(2); mixed, predominately antiparallel beta-sheet, order: 123465, strands 4 and 5 are parallel to each other
Hypothetical protein Ta1206 [102891] (1) can be divided into an N-terminal, tetramerisation all-beta subdomain and a C-terminal alpha+beta subdomain related by a circular permutation to the Y-family DNA-polymerase 'fingers' subdomain
alpha/beta-Hammerhead [54664] (5)
core: beta-BETA-alpha-beta-BETA-beta-alpha; contains a beta-hammerhead motif similar to that in barrel-sandwich hybrids
Rv2632c-like [143212] (1) lacks the N-terminal helix; dimerises via the N-terminal strand and the C-terminal helix with the formation of a single beta-sheet wrapped around an antiparallel coiled coil
Dimeric alpha+beta barrel [54909] (17) dimerizes through the beta-sheet; forms beta-sheet barrel, closed (n=8, S=12); dimers may assemble in higher oligomers
GlnB-like [54913] (4) form timeric structures with the orthogonally packed beta-sheets
Methyl-coenzyme M reductase subunits [55088] (2) each of the three different subunits, alpha, beta and gamma, contains this fold decorated with additional secondary structures
DOPA-like [143410] (1) probable biological unit is homodimer; the extra C-terminal strand, adjacent and antiparallel to strand 4, contributes to the dimerisation interface
CcmK-like [143414] (1) contains extra C-terminal helix; forms compact hexameric 'tiles' of hexagonal shape
Transposase IS200-like [143422] (1) contains extra N-terminal hairpin and C-terminal helix, both are involved in dimerization; there can be helix-swapping in the dimer
TTP0101/SSO1404-like [143430] (1) contains extra C-terminal beta-strand that integrates into the beta-sheet of the other subunit in the homodimer, a probable biological unit of this superfamily
PurS-like [109622] (1)
consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
PurS-like [82697] (2) segment-swapped dimer: the swapped segment is made of the first helix and second strand; a single long strand is formed by strands 2 and 3 of each subunit
Dystroglycan, domain 2 [111005] (1)
beta-alpha-beta-X-beta(2)-alpha(2)-beta; antiparallel beta-sheet, order 24153; topological similarity to the ferredoxin-like fold (scop_cf 54861)
Pseudouridine synthase [100877] (1)
consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
Pseudouridine synthase [55120] (4) the active site is the most conserved structural region of the superfamily and is located between the subdomains
Folate-binding domain [103024] (1)
duplication: consists of two beta(2)-alpha-beta(3)-alpha subdomains swapped with the first strands
Folate-binding domain [103025] (2) some topological similarity to Formylmethanofuran:tetrahydromethanopterin formyltransferase
THUMP domain [143436] (1)
contains mixed 8-stranded beta-sheet, folded into a half-barrel and covered with 4 helices on the outside; order 32148756; strands 5, 6 and 7 are parallel
AMMECR1-like [143446] (1)
duplication; contains two beta(2)-alpha-beta(2) structural repeats, swapped with C-terminal strands; extra N-terminal helix and C-terminal strand
Ribosomal protein L30p/L7e [55128] (1)
core: beta-alpha-beta-alpha-beta; antiparallel beta-sheet: order 312; some similarity to the ferredoxin-like fold
LigT-like [55143] (1)
duplication of beta-alpha-beta-alpha-beta motif: antiparallel beta sheet forms barrel (n=6, S=8) similar to the barrel of prokaryotic DNA topoisomerases I and III
CYTH-like phosphatases [55153] (1)
duplication of beta-alpha-beta(3) motif: antiparallel beta sheet forms wide barrel (n=8, S=16) with a channel running through it
Antiparallel beta/alpha barrel (PT-barrel) [143491] (1)
tandem repeat of five alpha(2)-beta(2) motifs; antiparallel beta-sheet barrel, closed; n=10, S=10; order 123456789A; there is a channel along the barrel axis
Prenyltransferase-like [143492] (1) the barrel channel harbours the substrate-binding site
ThrRS/AlaRS common domain [55186] (2) putative editing domain found in the N-terminal part of ThrRS, the C-terminal of AlaRS, and as a stand-alone protein; probable circular permutation of LuxS (d.185.1.2)
LuxS/MPP-like metallohydrolase [63411] (2) Share the same "active site motif" HxxEH located in the first core helix, but differ in one of the zinc-binding residues
IF3-like [55199] (7)
beta-alpha-beta-alpha-beta(2); 2 layers; mixed sheet 1243, strand 4 is antiparallel to the rest
PUG domain-like [143502] (1)
alpha(2)-beta-alpha(2)-beta(2)-alpha; cluster of helices with a small antiparallel beta-sheet on one side; order 132; topological similarity to the fold of an extended R3H domain (PDB 1whr)
TRCF domain-like [143516] (1)
beta-alpha(3)-beta(2)-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed beta sheet, order 12354, strands 1 and 2 are parallel; some topological similarity to the DCoH-like fold (scop_cf 55247)
Bacillus chorismate mutase-like [55297] (7)
core: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
YjgF-like [55298] (2) forms trimers with three closely packed beta-sheets; possibly related to the IspF (d.79.5) and 4'-phosphopantetheinyl transferase superfamilies (d.150.1)
IpsF-like [69765] (1) forms trimers with three closely packed beta-sheets; possible link between the YjgF-like (d.79.1) and 4'-phosphopantetheinyl transferase superfamilies (d.150.1)
FwdE-like [143555] (1) contains extra N-terminal and C-terminal structures
Hypothetical protein PF0899 [111056] (1)
alpha-beta-alpha-beta(4); 2 layers: a/b; mixed beta-sheet, order 23145, strands 1 and 3 are parallel; similar to the GAPDH C-terminal domain-like fold (scop_cf 55346)
GAS2 domain-like [143575] (1) this superfamily may include the most C-terminal domain of IBP39 (scop_fa 103410); the preceeding (middle) domain of IBP39 may be split and reassigned to the EF-hand superfamily (scop_sf 47473)
GK1464-like [143579] (1) dimer; pseudo barrel; the true dimeric barrel formation requires swapping of the C-ternimal beta-alpha units
YojJ-like [143596] (1)
alpha-beta-X-beta-alpha-beta(2)-alpha-beta(3); 3 layers: a/b/a; 7-stranded mixed beta-sheet, order 2431567; strands 1 and 3 are parallel to each other
STIV B116-like [143601] (1)
subunit fold consists of mixed 5-stranded beta-sheet, order:31452, strand 5 is antiparallel to the rest, with 3 helices on one side; dimerises with the formation of a single 10-stranded beta-sheet; strand 2 is in the dimer interface
TrkA C-terminal domain-like [116725] (1)
beta-X-beta(2)-X-beta-alpha; pseudo barrel capped by helix at one end; topological similarity to the HPr-like fold
T-fold [55619] (2)
beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1234 tunnel-shaped: its known members form wide oligomeric barrels different sizes
ApbE-like [143631] (1) duplication: contains two differently decorated beta(2)-alpha(2)-beta(2) subdomains, similar to other T-fold domains; probably does not form the tunnel-shaped oligomers
Cell cycle regulatory proteins [55636] (1)
beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1243 can form strand-exchange dimers
Roadblock/LC7 domain [103196] (1) alpha-beta(2)-alpha-beta(3)-alpha; structurally most similar to the SNARE-like superfamily with a circular permutation of the terminal helices
YeeU-like [143737] (1) beta(2)-alpha-beta(3); 2 layers, a/b; there is an oligomerization interface instead of the 'missing' helical layer
GlcG-like [143744] (1) alpha-beta(2)-alpha(3)-beta(2)-alpha; similar to the Roadblock/LC7 domain
YrdC/RibB [55820] (1)
core: alpha-beta(2)-alpha-beta-alpha(2)-beta(2)-alpha-beta-alpha-beta; 3 layers; mixed twisted sheet of 7 strands; order 7126354; strands 7 and 1 are parallel to each other
L28p-like [143799] (1)
unusual fold consisting of three beta-hairpins, that form a paper clip-like structure, and two helices; could have evolved from a glucocorticoid receptor-like zinc finger domain (scop_cf 57715)
L28p-like [143800] (2) In early ribosomal structures, L28p has been misinterpreted as L31p. in the Ribosomal protein L28p family, there are sequences containing two CxxC pairs. Threading these sequences into this fold brings the four cysteines in a similar site to the zinc-binding site of glucocorticoid receptor-like zinc fingers. In the Ribosomal protein L31p, there are also members with two CxxC pairs. However, these won't form a putative zinc-binding site in this fold. The L31p family are classified here temporarily, until its true fold is known
Bet v1-like [55961] (7) contains a single copy of this fold with a alpha-beta2 insertion after the first helix; there is a cavity between the beta-sheet and the long C-terminal helix
Rbstp2229 protein [111171] (1) forms segment-swapped dimers further organized in hexamers
RalF, C-terminal domain [118104] (1) contains a single copy of this fold decorated with additional structures
YwmB-like [143842] (1) duplication: tandem repeat of two circularly permuted motifs, alpha-beta-alpha-beta(4), assembled as in the TATA-box binding domain; forms a swapped dimer by exchanging the equivalent parts of the C-terminal motifs
XisI-like [143846] (1)
alpha-beta(4)-alpha-beta-alpha; 2 layers, a/b; antiparallel beta-sheet, order 1234, meander; the open side of beta-sheet provides dimerization interface
Molybdenum cofactor-binding domain [56003] (1) duplication: consists of 4 structural repeats arranged in 2 lobes contains one left-hand beta-alpha-beta unit per lobe
DeoB insert domain-like [143855] (1)
alpha-beta-X-beta(2)-alpha-beta(2); 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 2 and 5 are antiparallel to the rest
ERH-like [143874] (1)
beta(2)-alpha(2)-beta(2)-alpha; antiparallel beta-sheet, order:2134; helices are arranged in a bundle rather than packed agains beta-sheet; dimerises via with the formation of a flattened beta-barel: closed n=8, S=10
ATP-grasp [56058] (2)
Consists of two subdomains with different alpha+beta folds shares functional and structural similarities with the PIPK and protein kinase superfamilies
Hect, E3 ligase catalytic domain [56203] (1)
consists of two alpha+beta domains; the N-terminal domain is array of helices and beta-hairpins; the C-terminal domain is an a/b sandwich with one left-handed beta-alpha(n)-beta unit; conformational flexibility of domain orientation
Aldehyde ferredoxin oxidoreductase, N-terminal domain [56227] (1)
contains sandwich; duplication of alpha+beta motif with single mixed sheet motif: beta(2)-alpha-beta(3)-alpha-beta; strand order 216345, strands 1 and 6 are parallel
Archaeal IMP cyclohydrolase PurO [75569] (1) has a putative active site in the same topological location as the Ntn hydrolase but lacks the N-terminal nucleophile
DmpA/ArgJ-like [56265] (1)
duplication of beta(3)-alpha-beta-alpha motif; 4 layers: alpha/beta/beta/alpha
DmpA/ArgJ-like [56266] (2) convergent similarity to the Ntn amidohydrolases
ADC synthase [56321] (1)
duplication: contains four repeats of alpha-beta(2)-beta motif arranged in a 4 layer core structure: alpha/beta/beta/alpha; orthogonally packed beta-sheets
ADC synthase [56322] (1) the active site is formed by additional structures inserted into the core structure
Sulfolobus fructose-1,6-bisphosphatase-like [111248] (1)
4 layers: a/b/b/a; antiparallel beta sheets; similarities to ferredoxin-like fold (scop_cf 54861) in the N-terminal part (1-120) and to the Bacterial S-adenosylmethionine decarboxylase subunit (scop_fa 997656) in the C-terminal part (121-340)
UbiD C-terminal domain-like [143967] (1)
alpha-beta(2)-alpha-beta-alpha-beta(2); 3 layers, a/b/a; mixed beta-sheet, order: 12354, strands 2,3 and 5 are parallel to each other
IlvD/EDD N-terminal domain-like [143974] (1)
contains a large cluster of helices and a mixed beta-sheet of 4 strands; order 2134, strands 3 and 4 are parallel
SSo0622-like [111277] (1)
alpha(2)-beta(2)-alpha-beta-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel beta-sheet: order 21354; strands 1,3 and 5 and the C-terminal helix are longer than other secondary structures
SSo0622-like [111278] (1) the dimer, formed in the crystals, is a probable biological unit
Putative modulator of DNA gyrase, PmbA/TldD [111282] (1)
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)]
Oxysterol-binding protein-like [143999] (1)
core: large meander beta-sheet of 12 strands wrapped around the N-terminal (distorted) alpha-hairpin; some similarity to transmembrane beta-barrel proteins
CofE-like [144009] (1)
consists of two different domains; d1: beta-alpha-beta-alpha-beta(2)-alpha-beta, mixed sheet of 5 strands, order:15234, strands 2 and 3 are parralel; d2 is inserted in d1 after strand 2 and comprises a helix-turn-helix motif and two 3-stranded sheets
Peptidoglycan deacetylase N-terminal noncatalytic region [144014] (1)
consists of two different domains, d1: [alpha-beta(2)-alpha-beta(3); 3 layers: a/b/a; mixed beta-sheet, order 12345, strands 2 and 3 are parallel to each other with a left-handed crossover connection], d2: alpha-beta(3)-alpha; 2 layers; antiparallel beta-sheet, order 123]
