3BLX | pdb_00003blx

Yeast Isocitrate Dehydrogenase (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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
P	d3blxp_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
N	d3blxn_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
L	d3blxl_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
J	d3blxj_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H	d3blxh_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d3blxf_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d3blxd_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3blxb_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
O	d3blxo_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
M	d3blxm_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
K	d3blxk_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
I	d3blxi_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G	d3blxg_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d3blxe_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d3blxc_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d3blxa_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2 Family	Dimeric isocitrate & isopropylmalate dehydrogenases	8073660	4000791	SCOP2 (2022-06-29)
P	SCOP2 Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073661	3001375	SCOP2 (2022-06-29)
N	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073661	3001375	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073661	3001375	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073661	3001375	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073661	3001375	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073661	3001375	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073661	3001375	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073661	3001375	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076917	3001375	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076917	3001375	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076917	3001375	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076917	3001375	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076917	3001375	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076917	3001375	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076917	3001375	SCOP2B (2022-06-29)
A	SCOP2 Family	Dimeric isocitrate & isopropylmalate dehydrogenases	8076916	4000791	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8076917	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)
P	KWL1	e3blxP1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
N	KWL1	e3blxN1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
L	KWL1	e3blxL1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
J	KWL1	e3blxJ1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
H	KWL1	e3blxH1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
F	KWL1	e3blxF1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
D	KWL1	e3blxD1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
B	KWL1	e3blxB1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
O	KWL1	e3blxO1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
M	KWL1	e3blxM1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
K	KWL1	e3blxK1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
I	KWL1	e3blxI1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
G	KWL1	e3blxG1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
E	KWL1	e3blxE1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
C	KWL1	e3blxC1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)
A	KWL1	e3blxA1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: KWL1	ECOD (v295.2)

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 (4.3.0)
N	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
L	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
J	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
H	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
F	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
D	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)
O	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
M	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
K	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
I	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
G	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
E	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)
A	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
B, D, F, H, J B, D, F, H, J, L, N, P	PF00180	Isocitrate/isopropylmalate dehydrogenase (Iso_dh)	Isocitrate/isopropylmalate dehydrogenase		Domain
A, C, E, G, I A, C, 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, D, F, H, J B, D, F, H, J, L, N, P	Isocitrate dehydrogenase [NAD] subunit 2	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 oxoacid metabolic process glutamate family amino acid biosynthetic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process amino 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 oxoacid metabolic process glutamate family amino acid biosynthetic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process amino acid metabolic process L-glutamate biosynthetic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process glutamate metabolic process proteinogenic amino acid biosynthetic process small molecule metabolic process dicarboxylic acid biosynthetic process secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process alcohol 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
A, C, E, G, I A, C, E, G, I, K, M, O	Isocitrate dehydrogenase [NAD] subunit 1	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 oxoacid metabolic process glutamate family amino acid biosynthetic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process amino 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 oxoacid metabolic process glutamate family amino acid biosynthetic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process amino acid metabolic process L-glutamate biosynthetic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process glutamate metabolic process proteinogenic amino acid biosynthetic process small molecule metabolic process dicarboxylic acid biosynthetic process secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process alcohol 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 cytosol 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 cytosol membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membraneless organelle mitochondrial nucleoid mitochondrial intermembrane space organelle envelope lumen organelle envelope mitochondrial envelope

InterPro: Protein Family Classification InterPro Database Homepage

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.