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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: SH3
H: SH3
T: SH3
F: PAZ

PF02170 CL0010

Representatives:

e4ngdA1[A:902-1032] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; ligands: PEG,SO4 ; X-RAY DIFFRACTION 1.950Å

e1si2A1[A:224-349] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Eukaryotic translation initiation factor 2C 1 ; X-RAY DIFFRACTION 2.60Å

e2fflA2[A:150-254] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dicer ; ligands: MN ; X-RAY DIFFRACTION 3.33Å

e4nhaA1[A:902-992,A:1020-1032] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 3.4Å

e1t2sA1[A:1-123] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Argonaute 2 ; SOLUTION NMR

e1r6zA1[A:598-716] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chimera of Maltose-binding periplasmic protein and Argonaute 2 ; ligands: NI ; X-RAY DIFFRACTION 2.8Å

e7swfA2[A:333-393,A:425-449] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute 10 ; ELECTRON MICROSCOPY

e7svaA1[A:333-397,A:424-449] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute 10 ; ELECTRON MICROSCOPY

e1t2rA1[A:1-123] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Argonaute 2 ; SOLUTION NMR

e7swqA1[A:333-397,A:423-449] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute 10 ; ELECTRON MICROSCOPY

e1vynA1[A:4-120] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ARGONAUTE2 ; SOLUTION NMR

e1r6zZ1[Z:598-719] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chimera of Maltose-binding periplasmic protein and Argonaute 2 ; ligands: NI ; X-RAY DIFFRACTION 2.8Å

e1r6zP1[P:598-717] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chimera of Maltose-binding periplasmic protein and Argonaute 2 ; ligands: NI ; X-RAY DIFFRACTION 2.8Å

e1si3A1[A:224-349] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EUKARYOTIC TRANSLATION INITIATION FACTOR 2C 1 ; X-RAY DIFFRACTION 2.6Å

e1r4kA1[A:301-426] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Argonaute 1 ; SOLUTION NMR

e2xfmA1[A:276-395] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PIWI-LIKE PROTEIN 1 ; SOLUTION NMR

e3qirA1[A:2-116] Image Pymol Jmol Links: PDB, SCOP, CATH

Piwi-like protein 2 ; X-RAY DIFFRACTION 2.45Å

e3mj0A1[A:600-717] Image Pymol Jmol Links: PDB, SCOP, CATH

PROTEIN ARGONAUTE-2 ; X-RAY DIFFRACTION 2.31Å

e2l5cA1[A:266-399] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PIWI-LIKE PROTEIN 1 ; SOLUTION NMR

e2l5dA1[A:266-399] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PIWI-LIKE PROTEIN 1 ; SOLUTION NMR

e3o3iX1[X:276-393] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Piwi-like protein 1 ; X-RAY DIFFRACTION 2.800Å

e3o6eX1[X:277-393] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Piwi-like protein 1 ; X-RAY DIFFRACTION 2.900Å

e3o7vX1[X:277-393] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Piwi-like protein 1 ; X-RAY DIFFRACTION 2.100Å

e3o7xA1[A:386-501] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Piwi-like protein 2 ; X-RAY DIFFRACTION 2.920Å

e3o7xB1[B:386-501] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Piwi-like protein 2 ; X-RAY DIFFRACTION 2.920Å

e3o7xC1[C:386-501] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Piwi-like protein 2 ; X-RAY DIFFRACTION 2.920Å

e3o7xD1[D:388-501] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Piwi-like protein 2 ; X-RAY DIFFRACTION 2.920Å

e3qirB1[B:3-118] Image Pymol Jmol Links: PDB, SCOP, CATH

Piwi-like protein 2 ; X-RAY DIFFRACTION 2.45Å

e3qirC1[C:1-118] Image Pymol Jmol Links: PDB, SCOP, CATH

Piwi-like protein 2 ; X-RAY DIFFRACTION 2.45Å

e3qirD1[D:3-118] Image Pymol Jmol Links: PDB, SCOP, CATH

Piwi-like protein 2 ; X-RAY DIFFRACTION 2.45Å

e4kxtA3[A:225-349] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-1 ; X-RAY DIFFRACTION 2.294Å

e4olbA8[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN ARGONAUTE-2 ; X-RAY DIFFRACTION 2.9Å

e4ei3A6[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e2qvwA5[A:144-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GLP_546_48378_50642 ; X-RAY DIFFRACTION 3Å

e2qvwB5[B:144-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GLP_546_48378_50642 ; ligands: MN ; X-RAY DIFFRACTION 3Å

e4ei1A8[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4olaA3[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: IPA ; X-RAY DIFFRACTION 2.200Å

e4ngbA1[A:891-1014] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 2.250Å

e4ngcA1[A:891-1013] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 2.100Å

e4nh5A1[A:891-1014] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 2.550Å

e4nh6A1[A:891-1013] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 2.550Å

e4kreA10[A:222-344] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-1 ; X-RAY DIFFRACTION 1.750Å

e4nggA3[A:874-987] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; ligands: PO4 ; X-RAY DIFFRACTION 2.600Å

e4nh3A3[A:874-987] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 2.600Å

e4f3tA5[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.250Å

e2fflC4[C:144-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dicer ; ligands: MN ; X-RAY DIFFRACTION 3.33Å

e2fflD4[D:144-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dicer ; X-RAY DIFFRACTION 3.33Å

e2qvwC4[C:144-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GLP_546_48378_50642 ; ligands: MN ; X-RAY DIFFRACTION 3Å

e2qvwD4[D:144-247] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GLP_546_48378_50642 ; X-RAY DIFFRACTION 3Å

e4ngfA1[A:891-1014] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 3.100Å

e4ngfB1[B:891-1014] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 3.100Å

e4ngfC1[C:891-1014] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 3.100Å

e4ngfD1[D:891-1014] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Endoribonuclease Dicer ; X-RAY DIFFRACTION 3.100Å

e4krfA4[A:222-344] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-1 ; X-RAY DIFFRACTION 2.100Å

e4w5nA4[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.90Å

e4w5oA3[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: IPA,PO4 ; X-RAY DIFFRACTION 1.80Å

e4w5qA3[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 3.10Å

e4w5rA3[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: IPA ; X-RAY DIFFRACTION 2.50Å

e4w5tA3[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.50Å

e4z4cA2[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: PO4 ; X-RAY DIFFRACTION 2.30Å

e4z4dA4[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: IPA ; X-RAY DIFFRACTION 1.60Å

e4z4eA2[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: IPA ; X-RAY DIFFRACTION 1.80Å

e4z4fA1[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.80Å

e4z4gA4[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.70Å

e4z4hA4[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.50Å

e4z4iA5[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.80Å

e5ki6A3[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.15Å

e5js1A1[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.499Å

e5js2A5[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.95Å

e5guhA2[A:315-422] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PIWI ; X-RAY DIFFRACTION 2.40Å

e5t7bA4[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH

Protein argonaute-2 ; X-RAY DIFFRACTION 2.529Å

e5w6vA1[A:222-344] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-1 ; X-RAY DIFFRACTION 2.828Å

e5vm9A2[A:225-347] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-3 ; X-RAY DIFFRACTION 3.28Å

e5vm9C5[C:225-347] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-3 ; X-RAY DIFFRACTION 3.28Å

e6cbdA3[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: IPA,TRP ; X-RAY DIFFRACTION 2.2Å

e5weaA2[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 3.1Å

e6ra4A1[A:213-345] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: GOL ; X-RAY DIFFRACTION 1.900Å

e6ra4B1[B:212-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: GOL ; X-RAY DIFFRACTION 1.900Å

e6n4oA1[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.89Å

e6oonA5[A:214-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-4 ; X-RAY DIFFRACTION 1.9Å

e6mfnA1[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.50Å

e6mfrA4[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 3.59Å

e6mfrB3[B:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; ligands: PO4 ; X-RAY DIFFRACTION 3.59Å

e6nitA1[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 3.79Å

e6nitB3[B:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 3.79Å

e6mdzA2[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 3.40Å

e6mdzB5[B:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 3.40Å

e6kr6A1[A:261-367] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein piwi ; ligands: HG ; X-RAY DIFFRACTION 2.900Å

e7kx7A3[A:400-514] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Piwi-A ; ELECTRON MICROSCOPY

e7kx9A5[A:400-514] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Piwi-A ; ELECTRON MICROSCOPY

e7ki3A1[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 3Å

e7ki3D4[D:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 3Å

e8d71A4[A:227-351] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.5Å

e8d6jA5[A:224-346] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein argonaute-2 ; X-RAY DIFFRACTION 2.5Å

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