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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: ClpS-like

contains a HTH motif

X: DNA clamp
H: DNA clamp
T: DNA clamp
F: PCNA_C

PF02747 CL0060

Representatives:

e1ud9A2[A:127-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

DNA POLYMERASE SLIDING CLAMP A ; ligands: ZN ; X-RAY DIFFRACTION 1.68Å

e1rwzA2[A:123-244] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp ; X-RAY DIFFRACTION 1.8Å

e1iz5A2[A:126-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 1.80Å

e7st9H2[H:227-301,H:391-474] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA damage checkpoint control protein MEC3 ; ELECTRON MICROSCOPY

e1isqA2[A:126-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating Cell Nuclear Antigen ; X-RAY DIFFRACTION 2.30Å

e1iz5B2[B:126-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 1.80Å

e7stbH2[H:227-304,H:403-474] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA damage checkpoint control protein MEC3 ; ELECTRON MICROSCOPY

e1ge8A2[A:126-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROLIFERATION CELL NUCLEAR ANTIGEN ; X-RAY DIFFRACTION 2.00Å

e8dqwH2[H:227-301,H:391-474] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA damage checkpoint control protein MEC3 ; ELECTRON MICROSCOPY

e1iz4A2[A:126-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.0Å

e2ix2A2[A:131-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP B ; X-RAY DIFFRACTION 2.2Å

e2izoC2[C:119-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP B ; ligands: ZN ; X-RAY DIFFRACTION 2.800Å

e1rxzA2[A:123-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP ; X-RAY DIFFRACTION 2.0Å

e2hiiX2[X:119-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA1 (SSO0397) ; X-RAY DIFFRACTION 2.790Å

e1rxmA2[A:123-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP ; X-RAY DIFFRACTION 2.8Å

e1ud9B2[B:127-245] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA POLYMERASE SLIDING CLAMP A ; ligands: ZN ; X-RAY DIFFRACTION 1.68Å

e2hikA2[A:119-250] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA1 (SSO0397) ; X-RAY DIFFRACTION 3.300Å

e2hikL2[L:119-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA1 (SSO0397) ; X-RAY DIFFRACTION 3.300Å

e1ud9D2[D:127-245] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA POLYMERASE SLIDING CLAMP A ; ligands: ZN ; X-RAY DIFFRACTION 1.68Å

e1ud9C2[C:127-245] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA POLYMERASE SLIDING CLAMP A ; ligands: ZN ; X-RAY DIFFRACTION 1.68Å

e2hikX2[X:119-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA1 (SSO0397) ; X-RAY DIFFRACTION 3.300Å

e2ntiD2[D:119-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp B ; ligands: BR ; X-RAY DIFFRACTION 2.5Å

e3aixB2[B:128-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP B ; X-RAY DIFFRACTION 2.9Å

e2ntiA2[A:119-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp B ; ligands: BR ; X-RAY DIFFRACTION 2.5Å

e3aixA2[A:126-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP C ; ligands: SO4 ; X-RAY DIFFRACTION 2.9Å

e2ntiG2[G:119-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp B ; ligands: BR ; X-RAY DIFFRACTION 2.5Å

e3a2fB2[B:124-248] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA polymerase sliding clamp ; X-RAY DIFFRACTION 2.67Å

e3lx2A2[A:126-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp 2 ; ligands: SO4 ; X-RAY DIFFRACTION 2.400Å

e2io4A2[A:119-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp B ; ligands: MPD ; X-RAY DIFFRACTION 2.6Å

e2io4C2[C:119-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp B ; X-RAY DIFFRACTION 2.6Å

e3lx1A2[A:123-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp 1 ; ligands: SO4 ; X-RAY DIFFRACTION 2.000Å

e3fdsC2[C:119-249] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp B ; ligands: EDO,GOL,PEG,PGE ; X-RAY DIFFRACTION 2.050Å

e3hi8A2[A:123-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen PcnA ; X-RAY DIFFRACTION 3.20Å

e3p83A2[A:123-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp ; X-RAY DIFFRACTION 3.01Å

e2io4B2[B:116-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp C ; ligands: CA,MPD ; X-RAY DIFFRACTION 2.6Å

e2ix2C2[C:137-259] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP A ; X-RAY DIFFRACTION 2.2Å

e2izoB2[B:116-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP C ; ligands: MG,ZN ; X-RAY DIFFRACTION 2.800Å

e2ix2B2[B:115-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP C ; X-RAY DIFFRACTION 2.2Å

e2hiiB2[B:116-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA2 (SSO1047) ; X-RAY DIFFRACTION 2.790Å

e2hiiY2[Y:116-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA2 (SSO1047) ; X-RAY DIFFRACTION 2.790Å

e2hikB2[B:116-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA2 (SSO1047) ; X-RAY DIFFRACTION 3.300Å

e2hikM2[M:116-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA2 (SSO1047) ; X-RAY DIFFRACTION 3.300Å

e2hikY2[Y:116-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA2 (SSO1047) ; X-RAY DIFFRACTION 3.300Å

e2hiiC2[C:122-243] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA3 (SSO0405) ; X-RAY DIFFRACTION 2.790Å

e2hiiZ2[Z:122-243] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA3 (SSO0405) ; X-RAY DIFFRACTION 2.790Å

e2hikC2[C:122-243] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA3 (SSO0405) ; X-RAY DIFFRACTION 3.300Å

e2hikN2[N:122-243] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA3 (SSO0405) ; X-RAY DIFFRACTION 3.300Å

e2hikZ2[Z:122-243] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA3 (SSO0405) ; X-RAY DIFFRACTION 3.300Å

e2ntiE2[E:116-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp C ; ligands: BR ; X-RAY DIFFRACTION 2.5Å

e2ntiB2[B:116-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp C ; ligands: BR ; X-RAY DIFFRACTION 2.5Å

e2ntiH2[H:116-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp C ; ligands: 7PG,BR ; X-RAY DIFFRACTION 2.5Å

e2io4D2[D:116-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp C ; ligands: CA,MPD ; X-RAY DIFFRACTION 2.6Å

e3fdsD2[D:116-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp C ; ligands: EDO ; X-RAY DIFFRACTION 2.050Å

e2ijxA2[A:122-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP A ; ligands: EDO ; X-RAY DIFFRACTION 1.9Å

e2ijxB2[B:122-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP A ; ligands: EDO ; X-RAY DIFFRACTION 1.9Å

e2ijxC2[C:122-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP A ; ligands: EDO ; X-RAY DIFFRACTION 1.9Å

e2ijxD2[D:122-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP A ; ligands: EDO ; X-RAY DIFFRACTION 1.9Å

e2ntiF2[F:122-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp A ; ligands: BR ; X-RAY DIFFRACTION 2.5Å

e2ntiC2[C:122-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp A ; ligands: BR ; X-RAY DIFFRACTION 2.5Å

e2ntiI2[I:125-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp A ; ligands: BR ; X-RAY DIFFRACTION 2.5Å

e3ifvA1[A:123-243] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA ; ligands: NA ; X-RAY DIFFRACTION 2.0Å

e3ifvB1[B:120-243] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA ; ligands: NA ; X-RAY DIFFRACTION 2.0Å

e3ifvC2[C:123-243] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCNA ; ligands: NA ; X-RAY DIFFRACTION 2.0Å

e3hi8B2[B:123-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen PcnA ; X-RAY DIFFRACTION 3.20Å

e3hi8C2[C:123-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen PcnA ; X-RAY DIFFRACTION 3.20Å

e3hi8D2[D:123-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen PcnA ; X-RAY DIFFRACTION 3.20Å

e3hi8E2[E:123-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen PcnA ; X-RAY DIFFRACTION 3.20Å

e3hi8F2[F:123-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen PcnA ; X-RAY DIFFRACTION 3.20Å

e3p83B2[B:123-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp ; X-RAY DIFFRACTION 3.01Å

e3p83C2[C:123-243] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp ; X-RAY DIFFRACTION 3.01Å

e3aizA2[A:128-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP B ; X-RAY DIFFRACTION 2.8Å

e3aizB2[B:128-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP B ; X-RAY DIFFRACTION 2.8Å

e3aizC2[C:126-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP C ; ligands: SO4 ; X-RAY DIFFRACTION 2.8Å

e3aizD2[D:126-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP C ; ligands: SO4 ; X-RAY DIFFRACTION 2.8Å

e3lx2B2[B:126-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp 2 ; ligands: SO4 ; X-RAY DIFFRACTION 2.400Å

e3lx2C2[C:126-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp 2 ; X-RAY DIFFRACTION 2.400Å

e5hacA2[A:127-190,A:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.95Å

e5hacB2[B:127-190,B:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.95Å

e5hacC1[C:127-190,C:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.95Å

e5hacD2[D:127-190,D:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.95Å

e5hacE1[E:127-190,E:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.95Å

e5hacF1[F:127-190,F:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.95Å

e5aujA1[A:126-247] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA polymerase sliding clamp ; X-RAY DIFFRACTION 2.50Å

e5da7A1[A:123-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp 1, Proliferating cell nuclear antigen ; ligands: SO4 ; X-RAY DIFFRACTION 2.8Å

e5da7D2[D:123-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp 1, Proliferating cell nuclear antigen ; ligands: SO4 ; X-RAY DIFFRACTION 2.8Å

e5daiA1[A:123-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase sliding clamp 1 ; ligands: SO4 ; X-RAY DIFFRACTION 2.0Å

e5a6dA2[A:123-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP ; X-RAY DIFFRACTION 2.80Å

e5a6dB2[B:123-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA POLYMERASE SLIDING CLAMP ; X-RAY DIFFRACTION 2.80Å

e5b7oA2[A:127-185,A:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

e5b7oB1[B:127-185,B:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

e5b7oC2[C:127-185,C:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

e5b7oD1[D:127-185,D:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

e5b7oE1[E:127-185,E:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

e5b7oF2[F:127-185,F:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH

e5h0tA1[A:127-185,A:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen ; ligands: PEG ; X-RAY DIFFRACTION 2.73Å

e5h0tD2[D:127-185,D:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.73Å

e5h0tE2[E:127-185,E:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen ; ligands: PEG ; X-RAY DIFFRACTION 2.73Å

e5h0tB2[B:127-185,B:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.73Å

e5h0tC2[C:127-185,C:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.73Å

e5h0tF2[F:127-185,F:227-289] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.73Å

e1u7bA2[A:127-255] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROLIFERATING CELL NUCLEAR ANTIGEN ; X-RAY DIFFRACTION 1.88Å

e3pge.1[B:129-163,A:100-191] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proliferating cell nuclear antigen & SUMO-modified proliferating cell nuclear antigen ; X-RAY DIFFRACTION 2.8Å

e1plqA2[A:127-258] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) ; ligands: HG ; X-RAY DIFFRACTION

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.

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