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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

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

X: Carbon-nitrogen hydrolase-like
H: Metallo-dependent phosphatases
T: Metallo-dependent phosphatases
F: DNA_pol_E_B

PF04042 CL0163

Representatives:

e5vbnA2[A:84-121,A:245-527] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase epsilon subunit 2 ; ligands: SO4 ; X-RAY DIFFRACTION 2.35Å

e4y97C2[C:151-202,C:330-598] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; X-RAY DIFFRACTION 2.5Å

e8focC1[C:369-580,C:606-705] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8fodC1[C:369-580,C:606-705] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8foeC2[C:369-580,C:606-705] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8fohC2[C:369-580,C:606-704] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8fojC2[C:369-580,C:606-705] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8fokC2[C:369-580,C:606-705] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e3floC2[C:369-580,C:606-705] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ligands: SO4 ; X-RAY DIFFRACTION 2.5Å

e3floA2[A:369-580,A:606-705] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ligands: SO4 ; X-RAY DIFFRACTION 2.5Å

e3floE2[E:369-580,E:606-705] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ligands: SO4 ; X-RAY DIFFRACTION 2.5Å

e3floG2[G:369-580,G:606-705] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ligands: SO4 ; X-RAY DIFFRACTION 2.5Å

e3e0jA2[A:-3-41,A:180-465] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase subunit delta-2 ; X-RAY DIFFRACTION 3Å

e3e0jC2[C:-3-41,C:180-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase subunit delta-2 ; X-RAY DIFFRACTION 3Å

e3e0jE2[E:-3-41,E:180-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase subunit delta-2 ; X-RAY DIFFRACTION 3Å

e3e0jG2[G:-3-41,G:180-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase subunit delta-2 ; X-RAY DIFFRACTION 3Å

e4y97A1[A:157-202,A:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; X-RAY DIFFRACTION 2.5Å

e4y97E1[E:157-202,E:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; X-RAY DIFFRACTION 2.5Å

e4y97G2[G:157-202,G:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; X-RAY DIFFRACTION 2.5Å

e5exrD2[D:155-202,D:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; X-RAY DIFFRACTION 3.600Å

e5exrH2[H:155-202,H:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; X-RAY DIFFRACTION 3.600Å

e6hv8B2[B:170-203,B:349-556,B:598-688] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase epsilon subunit B ; ELECTRON MICROSCOPY

e6hv9B1[B:170-194,B:349-556,B:598-688] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase epsilon subunit B ; ELECTRON MICROSCOPY

e6hmfA1[A:152-206,A:338-619] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase II small subunit ; ligands: ACT,CAC,FE,ZN ; X-RAY DIFFRACTION 2.60Å

e6hmfB1[B:152-206,B:338-619] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase II small subunit ; ligands: ACT,CA,CAC,FE,ZN ; X-RAY DIFFRACTION 2.60Å

e6p1hB1[B:5-51,B:193-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta small subunit ; ELECTRON MICROSCOPY

e6s1mB2[B:1-41,B:180-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta subunit 2 ; ELECTRON MICROSCOPY

e6s1nB1[B:1-41,B:180-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta subunit 2 ; ELECTRON MICROSCOPY

e6s1oB2[B:1-41,B:180-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta subunit 2 ; ELECTRON MICROSCOPY

e6tnyB1[B:1-41,B:180-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta subunit 2 ; ELECTRON MICROSCOPY

e6tnzB2[B:1-41,B:180-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta subunit 2 ; ELECTRON MICROSCOPY

e6t8hA2[A:196-206,A:338-619] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase II small subunit ; ligands: FE,ZN ; ELECTRON MICROSCOPY

e6wjv22[2:170-203,2:349-556,2:598-688] Image Pymol Jmol Links: PDB, SCOP, CATHDOI

DNA polymerase epsilon subunit B ; ELECTRON MICROSCOPY

e6knbA2[A:286-320,A:451-735] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase II small subunit ; ligands: FE,ZN ; ELECTRON MICROSCOPY

e6v8pF1[F:-1-51,F:193-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta small subunit ; ELECTRON MICROSCOPY

e6kncA1[A:286-320,A:451-735] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase II small subunit ; ligands: FE,ZN ; ELECTRON MICROSCOPY

e6v93F1[F:-1-51,F:193-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta small subunit ; ELECTRON MICROSCOPY

e7kc0B1[B:6-51,B:193-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POL31 isoform 1 ; ELECTRON MICROSCOPY

e7lxdF1[F:0-51,F:193-486] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta small subunit ; ELECTRON MICROSCOPY

e7oplB1[B:155-202,B:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e7pmkR1[R:164-194,R:349-556,R:598-689] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase epsilon subunit B ; ELECTRON MICROSCOPY

e7pmnR1[R:164-194,R:349-556,R:598-689] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase epsilon subunit B ; ELECTRON MICROSCOPY

e7s0tF1[F:-2-51,F:193-487] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase delta small subunit ; ELECTRON MICROSCOPY

e8d0bG1[G:143-202,G:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8d0kG2[G:143-202,G:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e7u5cD1[D:155-202,D:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e7qhsF1[F:167-194,F:349-556,F:598-687] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase epsilon subunit B ; ELECTRON MICROSCOPY

e7z13F2[F:167-194,F:349-556,F:598-687] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase epsilon subunit B ; ELECTRON MICROSCOPY

e7z13M1[M:167-194,M:349-556,M:598-687] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase epsilon subunit B ; ELECTRON MICROSCOPY

e7uy8B1[B:307-595] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8g99B1[B:159-202,B:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8g9fB2[B:159-202,B:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8d9dD1[D:155-202,D:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase alpha subunit B ; ELECTRON MICROSCOPY

e8b9dA2[A:96-114,A:170-202,A:330-598] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

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 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