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X - Possible homology level

H - Homology level

T - Topology level

F - Family level

* - Provisional representative


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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

X: LuxS, MPP, ThrRS/AlaRS common domain

looks like an elaborated ferredoxin

X: a+b domain in type II DNA topoisomerase
H: a+b domain in type II DNA topoisomerase
T: a+b domain in type II DNA topoisomerase
F: DNA_topoisoIV

PF00521

Representatives:

e4cklA2[A:164-345] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA GYRASE SUBUNIT A ; ligands: SM8 ; X-RAY DIFFRACTION 2.05Å

e4cklB2[B:164-344] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA GYRASE SUBUNIT A ; X-RAY DIFFRACTION 2.05Å

e2xkjE3[E:1166-1344] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TOPOISOMERASE IV ; ligands: SO4 ; X-RAY DIFFRACTION 2.20Å

e1bjtA4[A:823-988] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TOPOISOMERASE II ; X-RAY DIFFRACTION 2.5Å

e2rgrA5[A:823-988] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 2 ; X-RAY DIFFRACTION 3.000Å

e4z2cA2[A:159-341] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

DNA gyrase subunit A ; X-RAY DIFFRACTION 3.03Å

e2xctU3[U:1162-1345] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A ; X-RAY DIFFRACTION 3.35Å

X: ClpS-like

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