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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: NMT1

PF09084 CL0177

Representatives:

e2x7pA1[A:1-86,A:185-306] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POSSIBLE THIAMINE BIOSYNTHESIS ENZYME ; ligands: ACY,AE3,CL,GOL ; X-RAY DIFFRACTION 2.34Å

e3e4rA2[A:112-209] Image Pymol Jmol Links: PDB, SCOP, CATH

Nitrate transport protein ; ligands: EPE ; X-RAY DIFFRACTION 2.003Å

e3uifA2[A:121-221] Image Pymol Jmol Links: PDB, SCOP, CATH

SULFONATE ABC TRANSPORTER, PERIPLASMIC SULFONATE-BINDING PROTEIN SSUA ; ligands: SO4 ; X-RAY DIFFRACTION 2.6Å

e2x26A1[A:107-212] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e3ksjA2[A:87-184] Image Pymol Jmol Links: PDB, SCOP, CATH

Nitrate transport protein ; ligands: MES ; X-RAY DIFFRACTION 2.000Å

e3ksxA2[A:109-209] Image Pymol Jmol Links: PDB, SCOP, CATH

Nitrate transport protein ; ligands: MPO,SO4 ; X-RAY DIFFRACTION 1.7Å

e2x7qA1[A:1-86,A:185-306] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POSSIBLE THIAMINE BIOSYNTHESIS ENZYME ; ligands: CA,GOL ; X-RAY DIFFRACTION 2.0Å

e4gvoA1[A:122-222] Image Pymol Jmol Links: PDB, SCOP, CATH

LMO2349 PROTEIN ; ligands: CSX,HIS ; X-RAY DIFFRACTION 1.45Å

e4gvoB1[B:122-222] Image Pymol Jmol Links: PDB, SCOP, CATH

LMO2349 PROTEIN ; ligands: CSX,HIS ; X-RAY DIFFRACTION 1.45Å

e4kqpA2[A:346-441] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamine ABC transporter permease and substrate binding protein protein ; ligands: GLN ; X-RAY DIFFRACTION 0.95Å

e4kr5A1[A:346-441] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamine ABC transporter permease and substrate binding protein protein ; ligands: P6G ; X-RAY DIFFRACTION 1.5Å

e4kr5B1[B:346-441] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamine ABC transporter permease and substrate binding protein protein ; ligands: P33,PE4,PG0 ; X-RAY DIFFRACTION 1.5Å

e2o1mA1[A:104-203] Image Pymol Jmol Links: PDB, SCOP, CATH

Probable amino-acid ABC transporter extracellular-binding protein ytmK ; ligands: SO4 ; X-RAY DIFFRACTION 2.0Å

e2o1mB1[B:104-203] Image Pymol Jmol Links: PDB, SCOP, CATH

Probable amino-acid ABC transporter extracellular-binding protein ytmK ; X-RAY DIFFRACTION 2.0Å

e4oenA1[A:353-447] Image Pymol Jmol Links: PDB, SCOP, CATH

SECOND SUBSTRATE BINDING DOMAIN OF PUTATIVE AMINO ACID ABC TRANSPORTER ; ligands: CL ; X-RAY DIFFRACTION 1.65Å

e4oenB1[B:353-447] Image Pymol Jmol Links: PDB, SCOP, CATH

SECOND SUBSTRATE BINDING DOMAIN OF PUTATIVE AMINO ACID ABC TRANSPORTER ; ligands: CL,SO4 ; X-RAY DIFFRACTION 1.65Å

e2v25B2[B:102-188] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MAJOR CELL-BINDING FACTOR ; ligands: ASP,ZN ; X-RAY DIFFRACTION 1.49Å

e4zv1A1[A:96-193] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AncQR ; ligands: ARG ; X-RAY DIFFRACTION 1.52Å

e4zv2A2[A:96-193] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AncQR ; ligands: GLN ; X-RAY DIFFRACTION 1.43Å

e6h30A2[A:346-442] Image Pymol Jmol Links: PDB, SCOP, CATH

Glutamine ABC transporter permease and substrate binding protein protein ; ligands: PE5,PEG ; X-RAY DIFFRACTION 2.8Å

e6h30B2[B:346-442] Image Pymol Jmol Links: PDB, SCOP, CATH

Glutamine ABC transporter permease and substrate binding protein protein ; ligands: PEG,PGE ; X-RAY DIFFRACTION 2.8Å

e4h65B1[B:3-103,B:137-307] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.6Å

e4nmyA1[A:3-99,A:184-301] Image Pymol Jmol Links: PDB, SCOP, CATH

ABC-TYPE TRANSPORT SYSTEM, EXTRACELLULAR SOLUTE-BINDING PROTEIN ; ligands: VIB ; X-RAY DIFFRACTION 1.9Å

e4nmyB1[B:3-99,B:184-301] Image Pymol Jmol Links: PDB, SCOP, CATH

ABC-TYPE TRANSPORT SYSTEM, EXTRACELLULAR SOLUTE-BINDING PROTEIN ; ligands: VIB ; X-RAY DIFFRACTION 1.9Å

e3qslB2[B:20-162] Image Pymol Jmol Links: PDB, SCOP, CATH

Putative exported protein ; ligands: CIT ; X-RAY DIFFRACTION 2.0Å

e4nmyA2[A:100-184] Image Pymol Jmol Links: PDB, SCOP, CATH

ABC-TYPE TRANSPORT SYSTEM, EXTRACELLULAR SOLUTE-BINDING PROTEIN ; ligands: VIB ; X-RAY DIFFRACTION 1.9Å

e4nmyB2[B:100-184] Image Pymol Jmol Links: PDB, SCOP, CATH

ABC-TYPE TRANSPORT SYSTEM, EXTRACELLULAR SOLUTE-BINDING PROTEIN ; ligands: VIB ; X-RAY DIFFRACTION 1.9Å

e4h67A1[A:4-98,A:196-345] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67C1[C:4-98,C:196-344] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67D2[D:4-98,D:196-338] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67F1[F:4-98,F:196-338] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h6dF1[F:4-98,F:196-338] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.9Å

e4h6dB2[B:4-98,B:196-338] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.9Å

e4h6dC1[C:4-98,C:196-338] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.9Å

e4h6dD1[D:4-98,D:196-338] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.9Å

e4h6dG2[G:4-98,G:196-338] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.9Å

e3ix1A1[A:29-125,A:207-329] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein ; ligands: NFM ; X-RAY DIFFRACTION 2.40Å

e3ix1B2[B:29-125,B:207-329] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein ; ligands: NFM ; X-RAY DIFFRACTION 2.40Å

e4h67A2[A:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67C2[C:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67D1[D:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67F2[F:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h6dF2[F:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.9Å

e4h6dB1[B:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.9Å

e4h6dC2[C:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.9Å

e4h6dD2[D:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.9Å

e4h6dG1[G:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.9Å

e3ix1A2[A:126-206] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein ; ligands: NFM ; X-RAY DIFFRACTION 2.40Å

e3ix1B1[B:126-206] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein ; ligands: NFM ; X-RAY DIFFRACTION 2.40Å

e4h65A1[A:4-103,A:137-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; X-RAY DIFFRACTION 2.6Å

e4h6dA1[A:4-98,A:196-302] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.9Å

e4h6dA2[A:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.9Å

e4h67B2[B:4-98,B:196-309,B:331-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.7Å

e4h67E2[E:3-98,E:196-308,E:332-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67G1[G:4-98,G:196-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67H2[H:4-98,H:196-309,H:331-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4esxA1[A:-2-98,A:196-307] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyrimidine biosynthesis enzyme THI13 ; X-RAY DIFFRACTION 2.200Å

e4esxB1[B:-1-98,B:196-307] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyrimidine biosynthesis enzyme THI13 ; X-RAY DIFFRACTION 2.200Å

e4eswA2[A:-2-98,A:196-339] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyrimidine biosynthesis enzyme THI13 ; ligands: CIT ; X-RAY DIFFRACTION 1.600Å

e4eswB1[B:-2-98,B:196-339] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyrimidine biosynthesis enzyme THI13 ; ligands: CIT ; X-RAY DIFFRACTION 1.600Å

e4h6dE1[E:4-98,E:196-308,E:329-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.9Å

e4h6dH2[H:4-98,H:196-335] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.9Å

e4h67B1[B:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.7Å

e4h67E1[E:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67G2[G:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4h67H1[H:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: SO4 ; X-RAY DIFFRACTION 2.7Å

e4esxA2[A:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyrimidine biosynthesis enzyme THI13 ; X-RAY DIFFRACTION 2.200Å

e4esxB2[B:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyrimidine biosynthesis enzyme THI13 ; X-RAY DIFFRACTION 2.200Å

e4eswA1[A:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyrimidine biosynthesis enzyme THI13 ; ligands: CIT ; X-RAY DIFFRACTION 1.600Å

e4eswB2[B:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyrimidine biosynthesis enzyme THI13 ; ligands: CIT ; X-RAY DIFFRACTION 1.600Å

e4h6dE2[E:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.9Å

e4h6dH1[H:99-195] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PYRIMIDINE PRECURSOR BIOSYNTHESIS ENZYME THI5 ; ligands: PLP ; X-RAY DIFFRACTION 2.9Å

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.

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