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: SH3
H: Chromo domain-like
T: Chromo domain-like
lacks the first strand in SH3
F: Chromo
Representatives:
e1pfbA1[A:23-77]
nonrep
Image
Pymol
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Polycomb protein ; ligands: ACY,BME,CL ; X-RAY DIFFRACTION 1.4Å
e2b2yA1[A:108-187]
nonrep
Image
Pymol
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Chromodomain-helicase-DNA-binding protein 1 ; X-RAY DIFFRACTION 2.350Å
e2b2yA2[A:13-107]
nonrep
Image
Pymol
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Chromodomain-helicase-DNA-binding protein 1 ; X-RAY DIFFRACTION 2.350Å
e3mwyW1[W:175-261]
nonrep
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Pymol
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Chromo domain-containing protein 1 ; X-RAY DIFFRACTION 3.7Å
e3mwyW2[W:262-347]
nonrep
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Pymol
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Chromo domain-containing protein 1 ; X-RAY DIFFRACTION 3.7Å
e1g6zA1[A:-2-69]
nonrep
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Pymol
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CLR4 PROTEIN ; SOLUTION NMR
e1guwA1[A:8-80]
nonrep
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CHROMOBOX PROTEIN HOMOLOG 1 ; SOLUTION NMR
e2dntA1[A:8-73]
nonrep
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Pymol
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Chromodomain protein, Y chromosome-like, isoform b ; 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