8GS5 | pdb_00008gs5

Crystal structure of a constitutively active mutant of human IDH3 holoenzyme in apo form

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth E]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
O [auth M]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
M [auth O]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
K [auth I]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
N [auth P]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076919	3001375	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076919	3001375	SCOP2B (2022-06-29)
F [auth H]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076919	3001375	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076919	3001375	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
L [auth J]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
P [auth N]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	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)
G [auth E]	Iso_dh	e8gs5E1	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)
O [auth M]	Iso_dh	e8gs5M2	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)
M [auth O]	Iso_dh	e8gs5O1	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)
K [auth I]	Iso_dh	e8gs5I1	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)
I [auth K]	Iso_dh	e8gs5K2	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)
E [auth G]	Iso_dh	e8gs5G1	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 [auth A]	Iso_dh	e8gs5A2	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)
A [auth C]	Iso_dh	e8gs5C2	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)
N [auth P]	Iso_dh	e8gs5P1	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)
J [auth L]	Iso_dh	e8gs5L1	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)
F [auth H]	Iso_dh	e8gs5H2	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 [auth D]	Iso_dh	e8gs5D2	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)
H [auth F]	Iso_dh	e8gs5F1	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)
L [auth J]	Iso_dh	e8gs5J1	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)
P [auth N]	Iso_dh	e8gs5N2	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)
D [auth B]	Iso_dh	e8gs5B1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], K [auth I], M [auth O], O [auth M]	PF00180	Isocitrate/isopropylmalate dehydrogenase (Iso_dh)	Isocitrate/isopropylmalate dehydrogenase		Domain
B [auth D], F [auth H], J [auth L], N [auth P]	PF00180	Isocitrate/isopropylmalate dehydrogenase (Iso_dh)	Isocitrate/isopropylmalate dehydrogenase		Domain
D [auth B], H [auth F], L [auth J], P [auth N]	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 [auth C], C [auth A], E [auth G], G [auth E], I [auth K], A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], K [auth I], M [auth O], O [auth M]	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial	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 (NAD+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD binding nucleoside phosphate 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 (NAD+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic 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 carbohydrate metabolic process secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process 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 carbohydrate metabolic process secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process alcohol metabolic process organic acid metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex isocitrate dehydrogenase complex (NAD+) tricarboxylic acid cycle heteromeric enzyme complex membrane-enclosed lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex isocitrate dehydrogenase complex (NAD+) tricarboxylic acid cycle heteromeric enzyme complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus
B [auth D], F [auth H], J [auth L], N [auth P]	Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide 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 (NAD+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD 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 carbohydrate metabolic process secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process 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 carbohydrate metabolic process secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process alcohol metabolic process organic acid metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen protein-containing complex catalytic complex oxidoreductase complex isocitrate dehydrogenase complex (NAD+) tricarboxylic acid cycle heteromeric enzyme complex mitochondrial matrix
D [auth B], H [auth F], L [auth J], P [auth N]	Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial	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 (NAD+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD binding nucleoside phosphate 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 (NAD+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding electron transfer activity	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 secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process 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 secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process alcohol metabolic process organic acid metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex isocitrate dehydrogenase complex (NAD+) tricarboxylic acid cycle heteromeric enzyme complex membrane-enclosed lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex isocitrate dehydrogenase complex (NAD+) tricarboxylic acid cycle heteromeric enzyme complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], K [auth I], M [auth O], O [auth M]	IPR024084	Isopropylmalate dehydrogenase-like domain	Domain
A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], K [auth I], M [auth O], O [auth M]	IPR019818	Isocitrate/isopropylmalate dehydrogenase, conserved site	Conserved Site
A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], K [auth I], M [auth O], O [auth M]	IPR004434	Isocitrate dehydrogenase NAD-dependent	Family
B [auth D], F [auth H], J [auth L], N [auth P]	IPR024084	Isopropylmalate dehydrogenase-like domain	Domain
B [auth D], F [auth H], J [auth L], N [auth P]	IPR019818	Isocitrate/isopropylmalate dehydrogenase, conserved site	Conserved Site
B [auth D], F [auth H], J [auth L], N [auth P]	IPR004434	Isocitrate dehydrogenase NAD-dependent	Family
D [auth B], H [auth F], L [auth J], P [auth N]	IPR024084	Isopropylmalate dehydrogenase-like domain	Domain
D [auth B], H [auth F], L [auth J], P [auth N]	IPR019818	Isocitrate/isopropylmalate dehydrogenase, conserved site	Conserved Site
D [auth B], H [auth F], L [auth J], P [auth N]	IPR004434	Isocitrate dehydrogenase NAD-dependent	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], A [auth C], C [auth A], E [auth G], G [auth E], I [auth K], K [auth I], M [auth O], O [auth M]	Pharos: P50213	astrocytic tumor glioblastoma malignant ependymoma osteoarthritis ovarian cancer plasma cell myeloma retinitis pigmentosa atopic eczema large cell medulloblastoma malignant glioma osteoarthritis susceptibility 1 pilocytic astrocytoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor malignant colon neoplasm astrocytic tumor glioblastoma malignant ependymoma osteoarthritis ovarian cancer plasma cell myeloma retinitis pigmentosa atopic eczema large cell medulloblastoma malignant glioma osteoarthritis susceptibility 1 pilocytic astrocytoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor malignant colon neoplasm medulloblastoma Osteoarthrosis Deformans pituitary cancer psoriasis
B [auth D], F [auth H], J [auth L], N [auth P]	Pharos: P51553	ovarian cancer Sjogren syndrome
D [auth B], H [auth F], L [auth J], P [auth N]	Pharos: O43837	retinitis pigmentosa retinitis pigmentosa 46 cone-rod dystrophy gastric cancer lymphoplasmacytic lymphoma Mitochondrial Diseases plasma cell myeloma gastric neoplasm malignant mesothelioma osteosarcoma psoriasis hereditary diffuse gastric adenocarcinoma ovarian cancer retinal degeneration

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.