8P5W | pdb_00008p5w

Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum following reaction with the 2-oxoglutarate analogue succinyl phosphonate

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Cas_Csm6_HEPN	e8p5wF1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cas_Csm6_HEPN	ECOD (develop294)
E	Cas_Csm6_HEPN	e8p5wE1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cas_Csm6_HEPN	ECOD (develop294)
D	Cas_Csm6_HEPN	e8p5wD1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cas_Csm6_HEPN	ECOD (develop294)
C	Cas_Csm6_HEPN	e8p5wC1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cas_Csm6_HEPN	ECOD (develop294)
B	Cas_Csm6_HEPN	e8p5wB1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cas_Csm6_HEPN	ECOD (develop294)
A	Cas_Csm6_HEPN	e8p5wA1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cas_Csm6_HEPN	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02779	Transketolase, pyrimidine binding domain (Transket_pyr)	Transketolase, pyrimidine binding domain	This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases.	Domain
A, B, C, D, E A, B, C, D, E, F	PF16870	2-oxoglutarate dehydrogenase C-terminal (OxoGdeHyase_C)	2-oxoglutarate dehydrogenase C-terminal	-	Family
A, B, C, D, E A, B, C, D, E, F	PF00676	Dehydrogenase E1 component (E1_dh)	Dehydrogenase E1 component	This family uses thiamine pyrophosphate as a cofactor. This family includes pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and 2-oxoisovalerate dehydrogenase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	2-oxoglutarate dehydrogenase E1/E2 component	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxoglutarate dehydrogenase (succinyl-transferring) activity catalytic activity S-succinyltransferase activity catalytic activity, acting on a protein acyltransferase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxoglutarate dehydrogenase (succinyl-transferring) activity catalytic activity S-succinyltransferase activity catalytic activity, acting on a protein acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity S-acyltransferase activity dihydrolipoyllysine-residue succinyltransferase activity succinyltransferase activity vitamin binding thiamine pyrophosphate binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex oxoglutarate dehydrogenase complex catalytic complex oxidoreductase complex transferase complex tricarboxylic acid cycle heteromeric enzyme complex alpha-ketoacid dehydrogenase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR042179	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR032106	2-oxoglutarate dehydrogenase E1 component, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011603	2-oxoglutarate dehydrogenase E1 component	Family
A, B, C, D, E A, B, C, D, E, F	IPR031717	2-oxoglutarate dehydrogenase E1 component/KDG, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001017	Dehydrogenase, E1 component	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.