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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

X: cradle loop barrel

Refs: Structure 14, 1489-1498; Current opinion in structural biology 18, 358-365

X: LigT-like
H: Prokaryotic type I DNA topoisomerase beta-barrel domain
T: Prokaryotic type I DNA topoisomerase beta-barrel domain
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:

e1mw9X1[X:215-280,X:404-472] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA Topoisomerase I ; ligands: SO4 ; X-RAY DIFFRACTION 1.67Å

e1d6mA1[A:216-287,A:415-485] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE III ; X-RAY DIFFRACTION 3.0Å

e1cy0A1[A:214-279,A:403-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 2.45Å

e1cy1A1[A:214-279,A:403-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; ligands: THP ; X-RAY DIFFRACTION 2.3Å

e1cy9A1[A:214-279,A:403-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 1.8Å

e1cyyB1[B:214-279,B:403-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 2.15Å

e1cy9B1[B:216-279,B:403-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 1.8Å

e1cyyA1[A:218-279,A:403-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 2.15Å

e2o19A4[A:217-288,A:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; X-RAY DIFFRACTION 2.450Å

e2o19B1[B:217-288,B:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; X-RAY DIFFRACTION 2.450Å

e2o54A1[A:217-288,A:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; X-RAY DIFFRACTION 2.479Å

e2o54B1[B:217-288,B:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; ligands: ACY ; X-RAY DIFFRACTION 2.479Å

e2o59A1[A:217-288,A:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; X-RAY DIFFRACTION 2.503Å

e2o59B1[B:217-288,B:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; X-RAY DIFFRACTION 2.503Å

e2o5cA1[A:217-288,A:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; X-RAY DIFFRACTION 2.350Å

e2o5cB1[B:217-288,B:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; X-RAY DIFFRACTION 2.350Å

e2o5eA1[A:217-288,A:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; X-RAY DIFFRACTION 2.500Å

e2o5eB1[B:217-288,B:416-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3 ; X-RAY DIFFRACTION 2.500Å

e4cgyA1[A:263-321,A:447-513] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE 3-ALPHA ; X-RAY DIFFRACTION 2.85Å

e4chtA4[A:263-321,A:447-513] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE 3-ALPHA ; X-RAY DIFFRACTION 3.25Å

e2gaiB4[B:187-241,B:374-440] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 1.7Å

e2gaiA3[A:187-241,A:374-440] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 1.7Å

e2gajB1[B:187-241,B:374-440] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 1.95Å

e2gajA4[A:187-241,A:374-440] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 1.95Å

e5d5hA7[A:214-303,A:433-512] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; ligands: GOL ; X-RAY DIFFRACTION 2.52Å

e3pwtA3[A:214-279,A:403-471] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA topoisomerase ; X-RAY DIFFRACTION 1.9Å

e5gvcA1[A:236-295,A:422-489] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3-beta-1 ; X-RAY DIFFRACTION 2.44Å

e5gvcB2[B:236-295,B:422-489] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3-beta-1 ; X-RAY DIFFRACTION 2.44Å

e5gveA3[A:236-295,A:422-489] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 3-beta-1 ; X-RAY DIFFRACTION 3.6Å

e6cq2A3[A:214-303,A:433-512] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; ligands: MG ; X-RAY DIFFRACTION 3.00Å

e5uj1A1[A:214-303,A:433-512] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; X-RAY DIFFRACTION 2.15Å

e5ujyA4[A:214-303,A:433-512] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; X-RAY DIFFRACTION 2.70Å

e5ujyB4[B:214-303,B:433-512] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; X-RAY DIFFRACTION 2.70Å

e6cqiA5[A:214-303,A:433-512] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; X-RAY DIFFRACTION 2.42Å

e6ozwA3[A:203-267,A:400-465] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; ligands: FMT ; X-RAY DIFFRACTION 2.060Å

e6pcmA4[A:212-300,A:427-512] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; ligands: SO4 ; X-RAY DIFFRACTION 3.10Å

e6pcmB5[B:212-300,B:427-512] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; ligands: SO4 ; X-RAY DIFFRACTION 3.10Å

e6k8nA4[A:221-277,A:405-473] Image Pymol Jmol Links: PDB, SCOP, CATH

topoisomerase III ; X-RAY DIFFRACTION 2.1Å

e6k8nB2[B:221-277,B:405-473] Image Pymol Jmol Links: PDB, SCOP, CATH

topoisomerase III ; X-RAY DIFFRACTION 2.1Å

e8czqA5[A:214-303,A:433-512] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; X-RAY DIFFRACTION 2.78Å

e8tfgA3[A:214-303,A:433-512] Image Pymol Jmol Links: PDB, SCOP, CATH

; ligands: ACT ; X-RAY DIFFRACTION 1.88Å

e1i7dA1[A:217-288,A:416-486] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE III ; X-RAY DIFFRACTION 2.05Å

e4ddtA1[A:773-812,A:938-1001] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Reverse gyrase ; X-RAY DIFFRACTION 3.20Å

e1gl9C6[C:731-770,C:893-954] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

REVERSE GYRASE ; X-RAY DIFFRACTION 3.200Å

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