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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: Ribosomal protein S5 domain 2-like
H: Ribosomal protein S5 domain 2-like
T: Ribosomal protein S5 domain 2-like
F: RNase_PH

PF01138 CL0329

Representatives:

e2je6A2[A:1-191] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 2 ; ligands: 1PE,PEG ; X-RAY DIFFRACTION 1.6Å

e2je6B2[B:8-155] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 1.6Å

e1r6lA2[A:1-151] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBONUCLEASE PH ; ligands: NHE,SO4 ; X-RAY DIFFRACTION 1.9Å

e1e3hA5[A:3-151] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GUANOSINE PENTAPHOSPHATE SYNTHETASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.600Å

e1e3hA6[A:346-482] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GUANOSINE PENTAPHOSPHATE SYNTHETASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.600Å

e1e3pA6[A:346-482] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: SO4,WO4 ; X-RAY DIFFRACTION 2.500Å

e3gcmA1[A:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: FLC,MG ; X-RAY DIFFRACTION 2.5Å

e3cdiA2[A:345-481] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polynucleotide phosphorylase ; X-RAY DIFFRACTION 2.6Å

e3h1cA5[A:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cB5[B:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cC5[C:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cG5[G:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cI5[I:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cK5[K:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cM5[M:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cO5[O:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cR5[R:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cT5[T:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cV5[V:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3h1cX5[X:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: WO4 ; X-RAY DIFFRACTION 3.57Å

e3gcmB5[B:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: 5GP,FLC,MG ; X-RAY DIFFRACTION 2.5Å

e3gcmC5[C:322-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: 5GP,FLC,MG ; X-RAY DIFFRACTION 2.5Å

e4aidA6[A:325-460] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: PO4 ; X-RAY DIFFRACTION 2.6Å

e3gllA8[A:323-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; X-RAY DIFFRACTION 2.7Å

e4aidB11[B:326-460] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: PO4 ; X-RAY DIFFRACTION 2.6Å

e4aimA13[A:326-460] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: PO4 ; X-RAY DIFFRACTION 3.3Å

e4aidC3[C:326-460] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: PO4 ; X-RAY DIFFRACTION 2.6Å

e4nbqA7[A:327-461] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: SO4 ; X-RAY DIFFRACTION 2.900Å

e4nbqB4[B:327-461] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: SO4 ; X-RAY DIFFRACTION 2.900Å

e4nbqC3[C:326-461] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: SO4 ; X-RAY DIFFRACTION 2.900Å

e4am3A3[A:325-460] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: PO4 ; X-RAY DIFFRACTION 3.0Å

e4am3B3[B:325-460] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: PO4 ; X-RAY DIFFRACTION 3.0Å

e4am3C3[C:325-460] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE ; ligands: PO4 ; X-RAY DIFFRACTION 3.0Å

e3gmeA1[A:323-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; X-RAY DIFFRACTION 2.4Å

e5xexA1[A:326-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: PPV ; X-RAY DIFFRACTION 2.2Å

e5xexB5[B:326-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: PPV ; X-RAY DIFFRACTION 2.2Å

e5xexC3[C:326-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: PPV ; X-RAY DIFFRACTION 2.2Å

e5xexD2[D:326-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: PPV ; X-RAY DIFFRACTION 2.2Å

e5xexE1[E:326-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: PPV ; X-RAY DIFFRACTION 2.2Å

e5xexF3[F:326-462] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ligands: PPV ; X-RAY DIFFRACTION 2.2Å

e3u1kA4[A:365-503] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL ; ligands: CIT ; X-RAY DIFFRACTION 2.13Å

e3u1kD5[D:365-503] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL ; ligands: CIT ; X-RAY DIFFRACTION 2.13Å

e3u1kB1[B:365-503] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL ; ligands: CIT ; X-RAY DIFFRACTION 2.13Å

e3u1kC5[C:365-503] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL ; ligands: CIT ; X-RAY DIFFRACTION 2.13Å

e6d6kA4[A:324-460] Image Pymol Jmol Links: PDB, SCOP, CATH

Polyribonucleotide nucleotidyltransferase ; X-RAY DIFFRACTION 2.500Å

e6d6kB5[B:324-460] Image Pymol Jmol Links: PDB, SCOP, CATH

Polyribonucleotide nucleotidyltransferase ; X-RAY DIFFRACTION 2.500Å

e5zf6B1[B:365-428,B:449-503] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase 1, mitochondrial ; X-RAY DIFFRACTION 2.796Å

e5zf6A2[A:365-427,A:449-503] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase 1, mitochondrial ; X-RAY DIFFRACTION 2.796Å

e7ld5A2[A:354-490] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7ld5B4[B:354-490] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7ld5C1[C:354-490] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7ogkA3[A:324-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7ogkB6[B:324-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7ogkC7[C:324-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7oglA5[A:324-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7oglB3[B:324-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7oglC6[C:324-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7ogmL5[L:324-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7ogmN6[N:324-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e7ogmO1[O:324-458] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Polyribonucleotide nucleotidyltransferase ; ELECTRON MICROSCOPY

e5k36C1[C:10-286] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Exosome complex component RRP43 ; ligands: SO4 ; X-RAY DIFFRACTION 3.100Å

e2nn6A2[A:1-184] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYMYOSITIS/SCLERODERMA AUTOANTIGEN 1 ; X-RAY DIFFRACTION 3.35Å

e2nn6C2[C:7-187] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE RRP43 ; X-RAY DIFFRACTION 3.35Å

e2nn6D2[D:25-146] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE RRP46 ; X-RAY DIFFRACTION 3.35Å

e2nn6E2[E:5-191] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE RRP42 ; X-RAY DIFFRACTION 3.35Å

e2nn6F2[F:29-72,F:92-175] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPONENT 6 ; X-RAY DIFFRACTION 3.35Å

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