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
X: beta-barrel domain in acetyl-CoA synthetase-like proteins
H: beta-barrel domain in acetyl-CoA synthetase-like proteins
T: beta-barrel domain in acetyl-CoA synthetase-like proteins
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.
Representatives:
e2y27A3[A:256-326]
* nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
PHENYLACETATE-COENZYME A LIGASE ; ligands: ATP,PG4,SCN ; X-RAY DIFFRACTION 1.60Å
e1pg4A1[A:437-515]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
acetyl-CoA synthetase ; ligands: PRX ; X-RAY DIFFRACTION 1.75Å
e4wd1A4[A:444-523]
* nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
Acetoacetate-CoA ligase ; ligands: EDO ; X-RAY DIFFRACTION 1.9Å
e3hguA2[A:283-354]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
EhpF ; X-RAY DIFFRACTION 1.950Å
e3cw9A1[A:324-400]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
4-CHLOROBENZOYL COA LIGASE ; ligands: AMP ; X-RAY DIFFRACTION 2.0Å
e1mdbA1[A:353-428]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
2,3-dihydroxybenzoate-AMP ligase ; ligands: AMP,SO4 ; X-RAY DIFFRACTION 2.15Å
e4isbA3[A:341-423]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
Long chain fatty acid CoA ligase FadD10 ; X-RAY DIFFRACTION 2.200Å
e4oxiA3[A:369-447]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
Enterobactin synthetase component F-related protein ; ligands: GAP ; X-RAY DIFFRACTION 2.26Å
e1v25A1[A:357-433]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
LONG-CHAIN-FATTY-ACID-COA SYNTHETASE ; ligands: ANP ; X-RAY DIFFRACTION 2.3Å
e5ey9B3[B:390-482]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
Long-chain-fatty-acid--AMP ligase FadD32 ; ligands: 5SV,GOL ; X-RAY DIFFRACTION 2.50Å
e5u2aA3[A:368-445]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH
AMP-dependent synthetase and ligase ; X-RAY DIFFRACTION 2.500Å
e1ultA1[A:357-433]
nonrep
Image
Pymol
Jmol Links:
PDB,
SCOP,
CATH, PubMed,
DOI
LONG CHAIN FATTY ACID-COA LIGASE ; X-RAY DIFFRACTION 2.55Å
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