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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: beta-Grasp
H: Ubiquitin-related
T: Ubiquitin-like
F: Plexin_RBD

PF20170 CL0072

Representatives:

e3hm6X2[X:1741-1890] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-B1 ; ligands: UNX ; X-RAY DIFFRACTION 2.400Å

e3h6nA1[A:1553-1656] Image Pymol Jmol Links: PDB, SCOP, CATH

Plexin-D1 ; ligands: ARS,UNX ; X-RAY DIFFRACTION 2.000Å

e3kuzA1[A:1196-1305] Image Pymol Jmol Links: PDB, SCOP, CATH

Plexin-C1 ; ligands: UNX ; X-RAY DIFFRACTION 2.300Å

e3q3jA1[A:1490-1600] Image Pymol Jmol Links: PDB, SCOP, CATH

Plexin-A2 ; ligands: UNX ; X-RAY DIFFRACTION 1.970Å

e4e71A1[A:1459-1561] Image Pymol Jmol Links: PDB, SCOP, CATH

Plexin-B2 ; ligands: NA ; X-RAY DIFFRACTION 2.260Å

e4e74A1[A:1496-1603] Image Pymol Jmol Links: PDB, SCOP, CATH

PLEXIN-A4 ; ligands: UNX ; X-RAY DIFFRACTION 1.58Å

e2r2oA1[A:1746-1852] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-B1 ; ligands: UNX ; X-RAY DIFFRACTION 2.000Å

e2r2oB1[B:1746-1852] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-B1 ; ligands: UNX ; X-RAY DIFFRACTION 2.000Å

e2rexA1[A:1746-1852] Image Pymol Jmol Links: PDB, SCOP, CATH

Plexin-B1 ; ligands: UNX ; X-RAY DIFFRACTION 2.300Å

e2rexC1[C:1746-1852] Image Pymol Jmol Links: PDB, SCOP, CATH

Plexin-B1 ; ligands: UNX ; X-RAY DIFFRACTION 2.300Å

e2jphA1[A:1-122] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-B1 ; SOLUTION NMR

e3kuzB1[B:1197-1305] Image Pymol Jmol Links: PDB, SCOP, CATH

Plexin-C1 ; ligands: UNX ; X-RAY DIFFRACTION 2.300Å

e3suaE1[E:1739-1854,E:1880-1881] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-B1 ; X-RAY DIFFRACTION 4.39Å

e3suaF1[F:1739-1854,F:1880-1881] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-B1 ; X-RAY DIFFRACTION 4.39Å

e3ig3A4[A:1471-1579,A:1626-1653] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plxna3 protein ; X-RAY DIFFRACTION 1.99Å

e4m8nD4[D:767-903] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PlexinC1 Intracellular Region ; X-RAY DIFFRACTION 3.294Å

e3suaD1[D:1739-1854,D:1880-1881] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-B1 ; X-RAY DIFFRACTION 4.39Å

e3rytB1[B:1486-1599] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PLEXIN-A1 ; X-RAY DIFFRACTION 3.58Å

e3su8X2[X:1739-1854,X:1880-1881] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-B1 ; X-RAY DIFFRACTION 3.20Å

e4m8nB2[B:775-913] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PlexinC1 Intracellular Region ; X-RAY DIFFRACTION 3.294Å

e5e6pA2[A:1457-1565] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-B2 ; X-RAY DIFFRACTION 3.20Å

e5v6rA2[A:1546-1671] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-D1 ; X-RAY DIFFRACTION 2.7Å

e5v6rB1[B:1546-1671] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-D1 ; X-RAY DIFFRACTION 2.7Å

e5v6tA2[A:1546-1671] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Plexin-D1 ; ligands: SO4 ; X-RAY DIFFRACTION 3.2Å

e4m8mA1[A:775-913] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GCN4 coiled-coil fused zebrafish PlexinC1 ; X-RAY DIFFRACTION 3.3Å

e4m8nA2[A:775-913] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PlexinC1 Intracellular Region ; X-RAY DIFFRACTION 3.294Å

e3rytA2[A:1496-1602,A:1651-1657] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PLEXIN-A1 ; X-RAY DIFFRACTION 3.58Å

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