3INM

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+)

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3inma_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	NADP-dependent isocitrate dehydrogenase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3inmb_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	NADP-dependent isocitrate dehydrogenase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3inmc_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	NADP-dependent isocitrate dehydrogenase	human (Homo sapiens ) [TaxId: 9606 ],	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	8039863	3001375	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8039863	3001375	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8039863	3001375	SCOP2B (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	Iso_dh	e3inmA2	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: Iso_dh	ECOD (1.6)
B	Iso_dh	e3inmB2	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: Iso_dh	ECOD (1.6)
C	Iso_dh	e3inmC1	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: Iso_dh	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
B	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
C	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00180	Isocitrate/isopropylmalate dehydrogenase (Iso_dh)	Isocitrate/isopropylmalate dehydrogenase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Isocitrate dehydrogenase [NADP] cytoplasmic	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding identical protein binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding identical protein binding protein binding protein homodimerization activity protein dimerization activity cell adhesion molecule binding cadherin 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 NAD binding	isocitrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process cellular metabolic process organic hydroxy compound metabolic process carboxylic acid metabolic process alcohol metabolic process organic acid metabolic process secondary alcohol metabolic process small molecule metabolic process metabolic process cellular process regulation of cellular process regulation of lipid metabolic process isocitrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process cellular metabolic process organic hydroxy compound metabolic process carboxylic acid metabolic process alcohol metabolic process organic acid metabolic process secondary alcohol metabolic process small molecule metabolic process metabolic process cellular process regulation of cellular process regulation of lipid metabolic process lipid biosynthetic process regulation of primary metabolic process phospholipid metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process regulation of biosynthetic process regulation of biological process biological regulation regulation of phospholipid metabolic process primary metabolic process regulation of cellular metabolic process phospholipid biosynthetic process regulation of phospholipid biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process regulation of phosphorus metabolic process regulation of lipid biosynthetic process regulation of metabolic process lipid metabolic process catabolic process phospholipid catabolic process organophosphate catabolic process cellular lipid catabolic process cellular catabolic process regulation of phospholipid catabolic process lipid catabolic process regulation of catabolic process regulation of lipid catabolic process regulation of cellular catabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process nucleotide metabolic process purine-containing compound metabolic process NADP metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process pyridine-containing compound metabolic process pyridine nucleotide metabolic process glutathione metabolic process sulfur compound metabolic process amide metabolic process cellular modified amino acid metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle cellular aldehyde metabolic process monocarboxylic acid metabolic process response to lipid response to stimulus response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to organic cyclic compound response to oxidative stress response to stress 2-oxoglutarate metabolic process dicarboxylic acid metabolic process developmental process multicellular organismal process gonad development reproductive system development reproductive process female gonad development sex differentiation animal organ development female sex differentiation development of primary female sexual characteristics developmental process involved in reproduction multicellular organism development development of primary sexual characteristics anatomical structure development reproductive structure development system development	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule endomembrane system intracellular organelle lumen organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle tertiary granule lumen tertiary granule vesicle lumen cytoplasmic vesicle lumen secretory granule lumen peroxisome microbody peroxisomal matrix microbody lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR024084	Isopropylmalate dehydrogenase-like domain	Domain
A, B, C	IPR004790	Isocitrate dehydrogenase NADP-dependent	Family
A, B, C	IPR019818	Isocitrate/isopropylmalate dehydrogenase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: O75874	Ollier disease oligodendroglioma cholangiocarcinoma Maffucci syndrome chondroma malignant glioma acute myeloid leukemia hemangioma childhood oligodendroglioma Neoplasm Recurrence, Local epithelioid hemangioma giant cell glioblastoma acute promyelocytic leukemia prostate cancer oligoastrocytoma Ollier disease oligodendroglioma cholangiocarcinoma Maffucci syndrome chondroma malignant glioma acute myeloid leukemia hemangioma childhood oligodendroglioma Neoplasm Recurrence, Local epithelioid hemangioma giant cell glioblastoma acute promyelocytic leukemia prostate cancer oligoastrocytoma glioblastoma adult oligodendroglioma gliosarcoma placental hemangioma primary myelofibrosis intrahepatic cholangiocarcinoma mixed glioma glioma hepatocellular carcinoma intramuscular hemangioma medulloblastoma colorectal cancer pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia glioma susceptibility 1 pituitary cancer anaplastic astrocytoma hematologic disease astrocytic tumor interstitial cystitis bile duct cancer lymphoplasmacytic lymphoma tuberculosis brain disease cancer metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria myelofibrosis congenital anemia exocrine pancreatic carcinoma pancreatic intraductal papillary-mucinous carcinoma peroxisomal disease anaplastic oligodendroglioma hematopoietic and lymphoid system neoplasm atypical teratoid rhabdoid tumor biliary tract neoplasm brain glioma malignant pancreatic neoplasm childhood acute lymphoblastic leukemia nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma aleukemic leukemia primitive neuroectodermal tumor benign neoplasm lung adenocarcinoma spinal cord disease bone disease

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.