6KDF | pdb_00006kdf

Crystal structure of the alpha beta heterodimer of human IDH3 in APO form.

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)
P	d6kdfp1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
P	d6kdfp2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
N	d6kdfn1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
N	d6kdfn2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d6kdfl1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d6kdfl2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d6kdfj1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d6kdfj2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6kdfh1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6kdfh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6kdff1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6kdff2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6kdfd1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6kdfd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d6kdfc1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d6kdfc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
O	d6kdfo_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M	d6kdfm_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d6kdfk_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d6kdfi_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6kdfg_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6kdfe1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6kdfe2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d6kdfa_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth B]	d6kdfb_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	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)
P	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8098166	3001375	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)
E	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 B]	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073659	3001375	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
P	e6kdfP1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
N	e6kdfN1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
L	e6kdfL1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
J	e6kdfJ1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
H	e6kdfH1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
F	e6kdfF1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
D	e6kdfD1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
B [auth C]	e6kdfC1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
O	e6kdfO1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
M	e6kdfM1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
K	e6kdfK1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
I	e6kdfI1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
G	e6kdfG1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
E	e6kdfE1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
C [auth A]	e6kdfA1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)
A [auth B]	e6kdfB1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: PQQ_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
N	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
L	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
J	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
H	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
F	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
D	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
B [auth C]	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
O	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
M	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
K	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
I	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
G	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
E	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
C [auth A]	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)
A [auth B]	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], D, F, H, J, B [auth C], D, F, H, J, L, N, P	PF00180	Isocitrate/isopropylmalate dehydrogenase (Iso_dh)	Isocitrate/isopropylmalate dehydrogenase		Domain
A [auth B], C [auth A], E, G, I, A [auth B], C [auth A], E, G, I, K, M, O	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
B [auth C], D, F, H, J, B [auth C], D, F, H, J, L, N, P	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
A [auth B], C [auth A], E, G, I, A [auth B], C [auth A], E, G, I, K, M, O	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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C], D, F, H, J, B [auth C], D, F, H, J, L, N, P	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
A [auth B], C [auth A], E, G, I, A [auth B], C [auth A], E, G, I, K, M, O	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