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
X: cradle loop barrel
Refs: Structure 14, 1489-1498; Current opinion in structural biology 18, 358-365
H: RIFT-related
T: Alanine racemase-C
125436, 2-crossover-3, 5-crossover-6
F: FAD_binding_6
Representatives:
e1krhA1[A:106-205]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
Benzoate 1,2-Dioxygenase Reductase ; ligands: FAD,SO4 ; X-RAY DIFFRACTION 1.5Å
e1fdrA1[A:2-100]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
FLAVODOXIN REDUCTASE ; ligands: FAD ; X-RAY DIFFRACTION 1.70Å
e1cqxA1[A:151-261]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
FLAVOHEMOPROTEIN ; ligands: FAD ; X-RAY DIFFRACTION 1.75Å
e1umkA1[A:30-153]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
NADH-CYTOCHROME B5 REDUCTASE ; ligands: FAD ; X-RAY DIFFRACTION 1.75Å
e1a8pA1[A:2-100]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
NADPH\:FERREDOXIN OXIDOREDUCTASE ; ligands: FAD ; X-RAY DIFFRACTION 2.0Å
e1ep3B1[B:2-102]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT) ; ligands: FAD ; X-RAY DIFFRACTION 2.1Å
e1qfjA1[A:1-97]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
PROTEIN (FLAVIN REDUCTASE) ; ligands: GOL ; X-RAY DIFFRACTION 2.2Å
e4ylfA1[A:1-97]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog ; ligands: FAD ; X-RAY DIFFRACTION 2.3Å
e1tvcA1[A:2-110]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
METHANE MONOOXYGENASE COMPONENT C ; ligands: FDA ; SOLUTION NMR
F: Unmapped domains
Pseudo group of domains that do not map to PFam family profiles. Domains inside should not be considered as in one family.
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
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