4E21 | pdb_00004e21

The crystal structure of 6-phosphogluconate dehydrogenase from Geobacter metallireducens

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	HSCB_C	e4e21B3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: HSCB_C	ECOD (v294.1)
A	HSCB_C	e4e21A5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: HSCB_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00393	6-phosphogluconate dehydrogenase, C-terminal domain (6PGD)	6-phosphogluconate dehydrogenase, C-terminal domain	This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase. The domain contains two structural repeats of 5 helices each.	Domain
A, B	PF03446	NAD binding domain of 6-phosphogluconate dehydrogenase (NAD_binding_2)	NAD binding domain of 6-phosphogluconate dehydrogenase	The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	6-phosphogluconate dehydrogenase (Decarboxylating)	binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding phosphogluconate dehydrogenase (decarboxylating) activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity	catabolic process small molecule metabolic process metabolic process cellular process organic acid catabolic process organic acid metabolic process small molecule catabolic process carbohydrate metabolic process oxoacid metabolic process D-gluconate metabolic process carboxylic acid metabolic process primary metabolic process monocarboxylic acid metabolic process nucleoside phosphate metabolic process catabolic process small molecule metabolic process metabolic process cellular process organic acid catabolic process organic acid metabolic process small molecule catabolic process carbohydrate metabolic process oxoacid metabolic process D-gluconate metabolic process carboxylic acid metabolic process primary metabolic process monocarboxylic acid metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process carbohydrate derivative metabolic process generation of precursor metabolites and energy glucose 6-phosphate metabolic process nucleotide metabolic process NADP+ metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process NADPH regeneration purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process phosphorus metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006115	6-phosphogluconate dehydrogenase, NADP-binding	Domain
A, B	IPR006114	6-phosphogluconate dehydrogenase, C-terminal	Domain
A, B	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR004849	6-phosphogluconate dehydrogenase, YqeC-type	Family
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A, B	IPR006183	6-phosphogluconate dehydrogenase	Family
A, B	IPR002204	3-hydroxyisobutyrate dehydrogenase-related, conserved site	Conserved Site

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.