5KVU

Crystal structure of isocitrate dehydrogenase-2 in complex with NADP(+) from Mycobacterium tuberculosis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5kvua_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Monomeric isocitrate dehydrogenase	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d5kvub_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Monomeric isocitrate dehydrogenase	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
C	d5kvuc_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Monomeric isocitrate dehydrogenase	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
D	d5kvud_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Monomeric isocitrate dehydrogenase	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8077773	3001375	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8077773	3001375	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8077773	3001375	SCOP2B (2022-06-29)
D	SCOP2 Family	Monomeric isocitrate dehydrogenase	8077772	4003133	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8077773	3001375	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	PF03971	e5kvuA2	A: a/b three-layered sandwiches	X: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	H: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	T: Isocitrate/Isopropylmalate dehydrogenase-like	F: PF03971	ECOD (1.6)
B	PF03971	e5kvuB2	A: a/b three-layered sandwiches	X: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	H: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	T: Isocitrate/Isopropylmalate dehydrogenase-like	F: PF03971	ECOD (1.6)
C	PF03971	e5kvuC3	A: a/b three-layered sandwiches	X: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	H: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	T: Isocitrate/Isopropylmalate dehydrogenase-like	F: PF03971	ECOD (1.6)
D	PF03971	e5kvuD1	A: a/b three-layered sandwiches	X: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	H: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	T: Isocitrate/Isopropylmalate dehydrogenase-like	F: PF03971	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03971	Monomeric isocitrate dehydrogenase (IDH)	Monomeric isocitrate dehydrogenase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Isocitrate dehydrogenase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding isocitrate dehydrogenase [NAD(P)+] activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor isocitrate dehydrogenase (NADP+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity identical protein binding protein binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding isocitrate dehydrogenase [NAD(P)+] activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor isocitrate dehydrogenase (NADP+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity identical protein binding protein binding protein homodimerization activity protein dimerization activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process primary metabolic process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process primary metabolic process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process organic substance metabolic process cellular aldehyde metabolic process small molecule metabolic process monocarboxylic acid metabolic process isocitrate metabolic process tricarboxylic acid metabolic process organic hydroxy compound metabolic process alcohol metabolic process secondary alcohol metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004436	Isocitrate dehydrogenase NADP-dependent, monomeric	Family

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 R01GM133198.