Evolutionary classification of protein domain structures
alpha arraysalpha-helix arrays with mainly perpendicular helices
alpha bundlesalpha-helix bundles with mainly parallel helices
alpha superhelicesrepeating alpha-helix hairpins form a superhelix
alpha duplicates or obligate multimersalpha duplicates or monomers associate together to form a compact domain
alpha complex topologyalpha domain with complex and unique topology that cannot be described as array or bundle or superhelix
beta barrelssingle beta-sheet folded upon itself to form a barrel
beta meanderssingle beta-sheet with mainly meander topology
beta sandwichestwo beta-sheets stacked together to form a sandwich
beta duplicates or obligate multimersbeta duplicates or monomers associate together to form a compact domain
beta complex topologybeta domains with complex and unique topology that cannot be described as barrel or sandwich or meander
a+b two layersone alpha-helix layer and one beta-sheet layer
looks like an elaborated ferredoxin
Pseudo group of domains that do not map to PFam family profiles. Domains inside should not be considered as in one family.
Representatives:
e1w23A1[A:260-360] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
PHOSPHOSERINE AMINOTRANSFERASE ; ligands: CL,MG,PEG ; X-RAY DIFFRACTION 1.080Å
e4uhmA2[A:349-448] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE ; ligands: GOL ; X-RAY DIFFRACTION 1.33Å
e1lc5A1[A:265-357] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE ; ligands: PO4 ; X-RAY DIFFRACTION 1.46Å
e1eluA1[A:300-393] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
L-CYSTEINE/L-CYSTINE C-S LYASE ; ligands: CSS,K,PDA ; X-RAY DIFFRACTION 1.55Å
e6cblA2[A:279-414] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Neamine transaminase NeoN ; ligands: DOW ; X-RAY DIFFRACTION 1.6Å
e2epjA2[A:325-434] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE ; X-RAY DIFFRACTION 1.7Å
e3f0hA3[A:258-357] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Aminotransferase ; ligands: UNL ; X-RAY DIFFRACTION 1.70Å
e3i4jA3[A:319-429] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Aminotransferase, class III ; X-RAY DIFFRACTION 1.70Å
e1vjoA1[A:281-381] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
alanine--glyoxylate aminotransferase ; X-RAY DIFFRACTION 1.700Å
e3ffrA3[A:260-361] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Phosphoserine aminotransferase SerC ; ligands: P33,SER ; X-RAY DIFFRACTION 1.75Å
e1m6sA1[A:248-343] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
L-allo-threonine aldolase ; X-RAY DIFFRACTION 1.8Å
e2x5fA3[A:328-428] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ASPARTATE_TYROSINE_PHENYLALANINE PYRIDOXAL-5' PHOSPHATE-DEPENDENT AMINOTRANSFERASE ; ligands: PO4 ; X-RAY DIFFRACTION 1.8Å
e3zrqA3[A:265-383] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
SERINE-PYRUVATE AMINOTRANSFERASE (AGXT) ; X-RAY DIFFRACTION 1.8Å
e4ritB2[B:366-480] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Pyridoxal-dependent decarboxylase ; ligands: CL,GOL ; X-RAY DIFFRACTION 1.8Å
e3g7qA3[A:301-416] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Valine-pyruvate aminotransferase ; ligands: CL,EDO ; X-RAY DIFFRACTION 1.80Å
e3pj0A3[A:0-22,A:253-358] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Lmo0305 protein ; ligands: MRD ; X-RAY DIFFRACTION 1.800Å
e3pj0C3[C:257-355] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Lmo0305 protein ; ligands: MRD,NA ; X-RAY DIFFRACTION 1.800Å
e2qmaA3[A:851-957] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
DIAMINOBUTYRATE-PYRUVATE TRANSAMINASE AND L-2,4- DIAMINOBUTYRATE DECARBOXYLASE ; X-RAY DIFFRACTION 1.81Å
e2r5eA1[A:313-429] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
KYNURENINE AMINOTRANSFERASE ; ligands: QLP ; X-RAY DIFFRACTION 1.84Å
e1c7nA1[A:290-394] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
CYSTALYSIN ; X-RAY DIFFRACTION 1.9Å
e2dr1A2[A:278-385] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
386AA LONG HYPOTHETICAL SERINE AMINOTRANSFERASE ; ligands: CL ; X-RAY DIFFRACTION 1.9Å
e2ykuA3[A:336-445] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
BETA-TRANSAMINASE ; ligands: EDO ; X-RAY DIFFRACTION 1.9Å
e1pmmA1[A:337-452] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
GLUTAMATE DECARBOXYLASE BETA ; X-RAY DIFFRACTION 2.0Å
e2x3lB2[B:265-359] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ORN/LYS/ARG DECARBOXYLASE FAMILY PROTEIN ; ligands: SM ; X-RAY DIFFRACTION 2.00Å
e1v72A1[A:258-350] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
ALDOLASE ; X-RAY DIFFRACTION 2.05Å
e2yriA2[A:250-352] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Aminotransferase, class V ; ligands: MMM ; X-RAY DIFFRACTION 2.05Å
e1wyuA1[A:341-437] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
GLYCINE DEHYDROGENASE (DECARBOXYLATING) SUBUNIT 1 ; X-RAY DIFFRACTION 2.1Å
e4lnjB2[B:244-332] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
LOW-SPECIFICITY L-THREONINE ALDOLASE ; X-RAY DIFFRACTION 2.1Å
e1svvA1[A:265-354] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
THREONINE ALDOLASE ; X-RAY DIFFRACTION 2.100Å
e1m32A1[A:264-365] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
2-aminoethylphosphonate-pyruvate aminotransferase ; ligands: POA ; X-RAY DIFFRACTION 2.15Å
e4xk1A1[A:261-360] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Phosphoserine aminotransferase ; ligands: FMT,GLU ; X-RAY DIFFRACTION 2.150Å
e3ezsA3[A:282-373] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
aminotransferase AspB ; X-RAY DIFFRACTION 2.19Å
e1iugA1[A:251-349] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
PUTATIVE ASPARTATE AMINOTRANSFERASE ; X-RAY DIFFRACTION 2.2Å
e3ke3A3[A:272-377] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Putative serine-pyruvate aminotransferase ; ligands: ACT,EDO,SO4 ; X-RAY DIFFRACTION 2.20Å
e2cy8A3[A:325-368,A:388-446] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
D-phenylglycine aminotransferase ; X-RAY DIFFRACTION 2.3Å
e3wy7D1[D:285-382] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
8-amino-7-oxononanoate synthase ; X-RAY DIFFRACTION 2.30Å
e5utsA2[A:328-470] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
C-S Lyase Egt2 ; ligands: FMT ; X-RAY DIFFRACTION 2.30Å
e2gsaA1[A:327-433] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
GLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE ; X-RAY DIFFRACTION 2.4Å
e2gb3A1[A:283-392] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
aspartate aminotransferase ; X-RAY DIFFRACTION 2.496Å
contains a HTH motif
a+b three layersone mainly antiparallel beta-sheet layer sandwiched between two alpha-helix layers
a+b four layerstwo beta-sheet layers sandwiched between two alpha-helix layers
a+b complex topologyalpha and beta domain with complex and unique topology that cannot be described in layers
a+b duplicates or obligate multimersalpha and beta duplicates or monomers associated together to form a compact domain
a/b barrelsrepeating beta-alpha units form a barrel
a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers
mixed a+b and a/balpha and beta domain consists of both a+b and a/b regions
few secondary structure elementsstabilized by cofactors or disulfides
extended segmentsextended, non-globular segments, frequently bind to other proteins to form complexes