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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: PLP-dependent transferases
H: PLP-dependent transferases
T: PLP-dependent transferases
F: DegT_DnrJ_EryC1

PF01041 CL0061

Representatives:

e2fnuA2[A:2-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

aminotransferase ; ligands: PMP,UD1 ; X-RAY DIFFRACTION 1.5Å

e1mdoA2[A:9-259] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ArnB aminotransferase ; ligands: PMP ; X-RAY DIFFRACTION 1.70Å

e4rxkB2[B:0-253] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

; ligands: GOL,PLP

e3gr9C2[C:1-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ColD ; X-RAY DIFFRACTION 2.2Å

e3gr9F2[F:3-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ColD ; X-RAY DIFFRACTION 2.2Å

e3gr9A2[A:5-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ColD ; ligands: AKG ; X-RAY DIFFRACTION 2.2Å

e3gr9D2[D:8-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ColD ; X-RAY DIFFRACTION 2.2Å

e3gr9G2[G:2-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ColD ; X-RAY DIFFRACTION 2.2Å

e3gr9H1[H:8-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ColD ; X-RAY DIFFRACTION 2.2Å

e3gr9B1[B:4-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ColD ; ligands: AKG ; X-RAY DIFFRACTION 2.2Å

e3gr9E2[E:5-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ColD ; ligands: AKG ; X-RAY DIFFRACTION 2.2Å

e2r0tA1[A:3-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyridoxamine 5-phosphate-dependent dehydrase ; ligands: PGU ; X-RAY DIFFRACTION 1.9Å

e2r0tB2[B:3-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyridoxamine 5-phosphate-dependent dehydrase ; ligands: PGU ; X-RAY DIFFRACTION 1.9Å

e3nysA2[A:1-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aminotransferase WbpE ; ligands: PLP ; X-RAY DIFFRACTION 1.45Å

e3frkB2[B:24-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

QDTB ; ligands: TQP ; X-RAY DIFFRACTION 2.15Å

e3frkA1[A:24-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

QDTB ; ligands: TQP ; X-RAY DIFFRACTION 2.15Å

e3nyuC1[C:2-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aminotransferase WbpE ; ligands: NA ; X-RAY DIFFRACTION 1.5Å

e3nyuB2[B:2-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aminotransferase WbpE ; ligands: EDO ; X-RAY DIFFRACTION 1.5Å

e3nyuD1[D:2-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aminotransferase WbpE ; X-RAY DIFFRACTION 1.5Å

e3nyuA2[A:1-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aminotransferase WbpE ; ligands: EDO ; X-RAY DIFFRACTION 1.5Å

e3nu8B2[B:1-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINOTRANSFERASE WBPE ; X-RAY DIFFRACTION 1.5Å

e3nu8A1[A:1-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINOTRANSFERASE WBPE ; X-RAY DIFFRACTION 1.5Å

e2gmuA1[A:-1-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative pyridoxamine 5-phosphate-dependent dehydrase, WbdK ; ligands: PDG ; X-RAY DIFFRACTION 1.9Å

e2gmuB2[B:-1-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative pyridoxamine 5-phosphate-dependent dehydrase, WbdK ; ligands: PDG ; X-RAY DIFFRACTION 1.9Å

e3b8xA1[A:3-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyridoxamine 5-phosphate-dependent dehydrase ; ligands: EDO,G4M,NA ; X-RAY DIFFRACTION 1.7Å

e3b8xB1[B:1-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyridoxamine 5-phosphate-dependent dehydrase ; ligands: G4M,NA ; X-RAY DIFFRACTION 1.7Å

e3nu7A2[A:2-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aminotransferase WbpE ; ligands: GOL,PMP ; X-RAY DIFFRACTION 1.95Å

e3nu7B2[B:1-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aminotransferase WbpE ; ligands: GOL,PMP ; X-RAY DIFFRACTION 1.95Å

e4zahC1[C:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

dTDP-4-amino-4,6-dideoxygalactose transaminase ; ligands: T5K ; X-RAY DIFFRACTION 2.240Å

e4zahF2[F:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

dTDP-4-amino-4,6-dideoxygalactose transaminase ; ligands: T5K ; X-RAY DIFFRACTION 2.240Å

e4zahA1[A:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

dTDP-4-amino-4,6-dideoxygalactose transaminase ; ligands: T5K ; X-RAY DIFFRACTION 2.240Å

e4zahD2[D:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

dTDP-4-amino-4,6-dideoxygalactose transaminase ; ligands: T5K ; X-RAY DIFFRACTION 2.240Å

e4zahH1[H:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

dTDP-4-amino-4,6-dideoxygalactose transaminase ; ligands: T5K ; X-RAY DIFFRACTION 2.240Å

e4zahG2[G:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

dTDP-4-amino-4,6-dideoxygalactose transaminase ; ligands: T5K ; X-RAY DIFFRACTION 2.240Å

e4zahB1[B:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

dTDP-4-amino-4,6-dideoxygalactose transaminase ; ligands: T5K ; X-RAY DIFFRACTION 2.240Å

e4zahE1[E:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

dTDP-4-amino-4,6-dideoxygalactose transaminase ; ligands: T5K ; X-RAY DIFFRACTION 2.240Å

e4wfpB1[B:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4wfpE2[E:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4wfpG1[G:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4wfpH2[H:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4wfpD2[D:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4wfpA1[A:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4wfpF2[F:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4wfpC2[C:0-250] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e3bcxB1[B:2-307] Image Pymol Jmol Links: PDB, SCOP, CATH

CDP-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase ; X-RAY DIFFRACTION 2.400Å

e3bcxA1[A:2-307] Image Pymol Jmol Links: PDB, SCOP, CATH

CDP-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase ; ligands: BEN,FE ; X-RAY DIFFRACTION 2.400Å

e3bb8B1[B:2-307] Image Pymol Jmol Links: PDB, SCOP, CATH

CDP-4-keto-6-deoxy-D-glucose-3-dehydrase ; ligands: PLP ; X-RAY DIFFRACTION 2.350Å

e3bb8A1[A:2-307] Image Pymol Jmol Links: PDB, SCOP, CATH

CDP-4-keto-6-deoxy-D-glucose-3-dehydrase ; ligands: PLP ; X-RAY DIFFRACTION 2.350Å

e4piwD2[D:2-250] Image Pymol Jmol Links: PDB, SCOP, CATH

TDP-4-keto-6-deoxy-D-glucose transaminase family protein ; X-RAY DIFFRACTION 2.7Å

e4piwA2[A:3-250] Image Pymol Jmol Links: PDB, SCOP, CATH

TDP-4-keto-6-deoxy-D-glucose transaminase family protein ; X-RAY DIFFRACTION 2.7Å

e4piwF1[F:3-250] Image Pymol Jmol Links: PDB, SCOP, CATH

TDP-4-keto-6-deoxy-D-glucose transaminase family protein ; X-RAY DIFFRACTION 2.7Å

e4piwC2[C:2-250] Image Pymol Jmol Links: PDB, SCOP, CATH

TDP-4-keto-6-deoxy-D-glucose transaminase family protein ; X-RAY DIFFRACTION 2.7Å

e4piwB2[B:1-250] Image Pymol Jmol Links: PDB, SCOP, CATH

TDP-4-keto-6-deoxy-D-glucose transaminase family protein ; X-RAY DIFFRACTION 2.7Å

e4piwE1[E:1-250] Image Pymol Jmol Links: PDB, SCOP, CATH

TDP-4-keto-6-deoxy-D-glucose transaminase family protein ; X-RAY DIFFRACTION 2.7Å

e4piwG2[G:1-250] Image Pymol Jmol Links: PDB, SCOP, CATH

TDP-4-keto-6-deoxy-D-glucose transaminase family protein ; X-RAY DIFFRACTION 2.7Å

e4piwH2[H:1-250] Image Pymol Jmol Links: PDB, SCOP, CATH

TDP-4-keto-6-deoxy-D-glucose transaminase family protein ; X-RAY DIFFRACTION 2.7Å

e3nubA1[A:1-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINOTRANSFERASE WBPE ; ligands: GOL,SO4,UD0 ; X-RAY DIFFRACTION 1.9Å

e3nubB1[B:1-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINOTRANSFERASE WBPE ; ligands: GOL,UD0 ; X-RAY DIFFRACTION 1.9Å

e2gmsA1[A:-1-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative pyridoxamine 5-phosphate-dependent dehydrase, Wbdk ; ligands: P0P ; X-RAY DIFFRACTION 1.8Å

e2gmsB1[B:0-266] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative pyridoxamine 5-phosphate-dependent dehydrase, Wbdk ; ligands: P0P ; X-RAY DIFFRACTION 1.8Å

e3nytA1[A:1-245] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aminotransferase WbpE ; ligands: ULP ; X-RAY DIFFRACTION 1.30Å

e5u23D1[D:13-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative aminotransferase ; ligands: EDO,TQP ; X-RAY DIFFRACTION 1.45Å

e4k2mA1[A:69-308] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

NTD biosynthesis operon protein NtdA ; ligands: ACT,EDO,O1G ; X-RAY DIFFRACTION 1.710Å

e1o69A2[A:12-244] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

aminotransferase ; ligands: BME,X04 ; X-RAY DIFFRACTION 1.85Å

e1b9hA2[A:5-253] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (3-AMINO-5-HYDROXYBENZOIC ACID SYNTHASE) ; ligands: PLP ; X-RAY DIFFRACTION 2.0Å

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