2PGD

THE STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE REFINED AT 2 ANGSTROMS RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2pgda1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	6-phosphogluconate dehydrogenase (6PGD)	sheep (Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
A	d2pgda2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	6-phosphogluconate dehydrogenase	sheep (Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Hydroxyisobutyrate dehydrogenase/6-phosphogluconate dehydrogenase-like	8001111	4000072	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	6-phosphogluconate dehydrogenase-like	8017573	3000048	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	6PGD	e2pgdA1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 6PGD	ECOD (1.6)
A	NAD_binding_2	e2pgdA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
A	1.20.5.320	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	6-Phosphogluconate Dehydrogenase, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	6-PHOSPHOGLUCONATE DEHYDROGENASE	binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound 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	carbohydrate metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process aldonic acid metabolic process D-gluconate metabolic process metabolic process small molecule metabolic process cellular process monocarboxylic acid metabolic process carbohydrate derivative metabolic process glucose 6-phosphate metabolic process carbohydrate metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process aldonic acid metabolic process D-gluconate metabolic process metabolic process small molecule metabolic process cellular process monocarboxylic acid metabolic process carbohydrate derivative metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process generation of precursor metabolites and energy nucleotide metabolic process purine-containing compound metabolic process NADP metabolic process NADPH regeneration organophosphate metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006115	6-phosphogluconate dehydrogenase, NADP-binding	Domain
A	IPR006114	6-phosphogluconate dehydrogenase, C-terminal	Domain
A	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A	IPR006184	6-phosphogluconate-binding site	Binding Site
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR006113	6-phosphogluconate dehydrogenase, decarboxylating	Family
A	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A	IPR006183	6-phosphogluconate dehydrogenase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	phosphogluconate dehydrogenase (decarboxylating) M-CSA #889	The enzyme participates in the oxidative branch of the pentose phosphate pathway, whose main purpose is to produce NADPH and pentose for biosynthetic reactions. It catalyses the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH.	Defined by 5 residues: SER:A-128LYS:A-183HIS:A-186ASN:A-187GLU:A-190 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.1.44 (PDB Primary Data) Search M-CSA Motif + EC 1.1.1.44

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.