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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

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

X: Periplasmic binding protein-like II
H: Periplasmic binding protein-like II
T: Periplasmic binding protein-like II
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.

Representatives:

e4mncA1[A:28-145,A:233-332] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TRAP dicarboxylate transporter-DctP subunit ; ligands: 173,SO4 ; X-RAY DIFFRACTION 1.050Å

e1q35A2[A:1-100,A:231-318] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

IRON BINDING PROTEIN FBPA ; ligands: EDO,FMT ; X-RAY DIFFRACTION 1.2Å

e1mqiA2[A:109-218] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

glutamate receptor 2 ; ligands: FWD ; X-RAY DIFFRACTION 1.35Å

e1pb7A2[A:144-248] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

N-methyl-D-aspartate Receptor Subunit 1 ; ligands: GLY ; X-RAY DIFFRACTION 1.35Å

e2ia4B2[B:129-279] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Putative periplasmic binding transport protein ; ligands: GLU,TRS ; X-RAY DIFFRACTION 1.50Å

e1ii5A3[A:95-187] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Slr1257 protein ; ligands: GLU ; X-RAY DIFFRACTION 1.6Å

e1j1nA2[A:1-132,A:311-492] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ALGQ2 ; X-RAY DIFFRACTION 1.6Å

e1j1nA3[A:133-310] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ALGQ2 ; ligands: CA ; X-RAY DIFFRACTION 1.6Å

e2p0sA1[A:48-183] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

ABC TRANSPORTER, PERMEASE PROTEIN, PUTATIVE ; ligands: ACT,FMT,MG ; X-RAY DIFFRACTION 1.6Å

e6r88D1[D:101-201] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamate receptor 3.3,Glutamate receptor 3.3 ; ligands: GLY,SO4 ; X-RAY DIFFRACTION 1.600Å

e2a5sA2[A:134-243] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

N-methyl-D-aspartate receptor NMDAR2A subunit ; ligands: GLU ; X-RAY DIFFRACTION 1.70Å

e5ixpA2[A:157-313] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Extracellular solute-binding protein family 1 ; ligands: FMT ; X-RAY DIFFRACTION 1.730Å

e6gz1A1[A:184-285] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HTH-type transcriptional regulator LeuO ; ligands: SO4 ; X-RAY DIFFRACTION 1.74Å

e6gz1A2[A:112-183,A:286-316] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HTH-type transcriptional regulator LeuO ; X-RAY DIFFRACTION 1.74Å

e4z9nB2[B:103-204] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Amino acid ABC transporter, periplasmic amino acid-binding protein ; ligands: EDO,GSH ; X-RAY DIFFRACTION 1.745Å

e2x26A2[A:25-106,A:208-332] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PERIPLASMIC ALIPHATIC SULPHONATES-BINDING PROTEIN ; ligands: GOL ; X-RAY DIFFRACTION 1.75Å

e3hn0A2[A:103-200] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Nitrate transport protein ; ligands: EDO ; X-RAY DIFFRACTION 1.75Å

e3hn0B1[B:21-102,B:201-300] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Nitrate transport protein ; ligands: EDO,PEG ; X-RAY DIFFRACTION 1.75Å

e3hn0A3[A:23-108,A:207-302] Image Pymol Jmol Links: PDB, SCOP, CATH

Nitrate transport protein ; ligands: EDO,PEG,PO4 ; X-RAY DIFFRACTION 1.75Å

e2de2A2[A:2-113] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DIBENZOTHIOPHENE DESULFURIZATION ENZYME B ; ligands: GOL ; X-RAY DIFFRACTION 1.800Å

e4p0iB2[B:115-237] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Nopaline-binding periplasmic protein ; X-RAY DIFFRACTION 1.89Å

e5ub3B1[B:31-114,B:190-192,B:239-309] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Phosphate-binding protein ; ligands: CL ; X-RAY DIFFRACTION 1.9Å

e2v3qA2[A:1-90,A:298-376] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HUMAN PHOSPHATE BINDING PROTEIN ; ligands: EDO,GOL,PO4 ; X-RAY DIFFRACTION 1.90Å

e5sv6A2[A:117-239] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Extracellular solute-binding protein, family 3 ; ligands: BR ; X-RAY DIFFRACTION 1.92Å

e1xt8A3[A:109-202] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

putative amino-acid transporter periplasmic solute-binding protein ; ligands: CYS ; X-RAY DIFFRACTION 2.00Å

e6l33B1[B:171-271] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MexT protein ; ligands: SO4 ; X-RAY DIFFRACTION 2.00Å

e5bwjC1[C:26-109,C:208-237] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Sensory transduction histidine kinase, putative ; X-RAY DIFFRACTION 2.05Å

e5bwjC2[C:110-207] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Sensory transduction histidine kinase, putative ; ligands: NO3 ; X-RAY DIFFRACTION 2.05Å

e3n26A2[A:120-211] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINO ACID ABC TRANSPORTER, PERIPLASMIC AMINO ACID-BINDING PROTEIN ; ligands: ARG ; X-RAY DIFFRACTION 2.1Å

e1uthA2[A:169-271] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

LYSR-TYPE REGULATORY PROTEIN ; ligands: SCN ; X-RAY DIFFRACTION 2.2Å

e6onpA2[A:116-229] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

periplasmic binding protein XoxJ ; ligands: EDO ; X-RAY DIFFRACTION 2.27Å

e5jkqB1[B:20-194,B:293-302] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PfVFT1 ; ligands: SO4 ; X-RAY DIFFRACTION 2.35Å

e5jkqB2[B:195-292] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PfVFT1 ; X-RAY DIFFRACTION 2.35Å

e2grvC1[C:25-61,C:170-276,C:567-599] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

LpqW ; X-RAY DIFFRACTION 2.4Å

e3oxnA2[A:188-289] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Putative transcriptional regulator, LysR family ; X-RAY DIFFRACTION 2.4Å

e5l9pB1[B:11-129,B:260-352] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

periplasmic binding protein ; ligands: SO4 ; X-RAY DIFFRACTION 2.54Å

e5ipwA1[A:27-107,A:216-359,A:622-659] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative ; X-RAY DIFFRACTION 2.6Å

e5gzsA2[A:123-208] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GGDEF family protein ; ligands: ARG ; X-RAY DIFFRACTION 2.601Å

e5gzsA4[A:356-456] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GGDEF family protein ; X-RAY DIFFRACTION 2.601Å

e3ispB2[B:93-164,B:263-295] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HTH-type transcriptional regulator Rv1985c/MT2039 ; X-RAY DIFFRACTION 2.7Å

e3ispB3[B:165-262] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HTH-type transcriptional regulator Rv1985c/MT2039 ; X-RAY DIFFRACTION 2.7Å

e4hcwA2[A:5-118,A:260-356] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

thiaminase-I ; X-RAY DIFFRACTION 2.7Å

e4rnsA1[A:169-273] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PCP degradation transcriptional activation protein ; X-RAY DIFFRACTION 2.7Å

e3kg2A5[A:498-506,A:631-730] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamate receptor 2 ; ligands: ZK1 ; X-RAY DIFFRACTION 3.600Å

e4pe5B5[B:529-539,B:660-761] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamate receptor ionotropic, NMDA 2B ; ligands: GLU,GLY,NAG ; X-RAY DIFFRACTION 3.950Å

e4pe5C5[C:536-548,C:659-756] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamate receptor ionotropic, NMDA 1 ; ligands: GLU,GLY ; X-RAY DIFFRACTION 3.950Å

e5l2eA4[A:543-551,A:664-768] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2 ; X-RAY DIFFRACTION 4.15Å

e1a99A3[A:29-135,A:277-369] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PUTRESCINE-BINDING PROTEIN ; ligands: PUT ; X-RAY DIFFRACTION

e1lstA3[A:91-190] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

LYSINE, ARGININE, ORNITHINE-BINDING PROTEIN ; ligands: LYS ; X-RAY DIFFRACTION

e1sbpA2[A:1-94,A:220-309] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

SULFATE-BINDING PROTEIN ; ligands: SO4 ; X-RAY DIFFRACTION

e1wdnA3[A:88-183] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GLUTAMINE BINDING PROTEIN ; ligands: GLN ; X-RAY DIFFRACTION

e4uqqA6[A:628-731] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 2 ; ligands: GLU ; ELECTRON MICROSCOPY

e8e93D2[D:651-807] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamate receptor ionotropic, NMDA 2C ; ELECTRON MICROSCOPY

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