3R8W

Structure of 3-isopropylmalate dehydrogenase isoform 2 from Arabidopsis thaliana at 2.2 angstrom resolution

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)
A	d3r8wa_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d3r8wb_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d3r8wc_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d3r8wd_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	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	8073665	3001375	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073665	3001375	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073665	3001375	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8073665	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	e3r8wA1	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	e3r8wB1	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	e3r8wC2	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	Iso_dh	e3r8wD2	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)
D	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, D	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, D	3-isopropylmalate dehydrogenase 2, chloroplastic	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding identical protein binding protein binding protein homodimerization activity protein dimerization activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 3-isopropylmalate dehydrogenase activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity	developmental process multicellular organism development multicellular organismal process gametophyte development anatomical structure development embryo sac development pyruvate family amino acid metabolic process oxoacid metabolic process pyruvate family amino acid biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process developmental process multicellular organism development multicellular organismal process gametophyte development anatomical structure development embryo sac development pyruvate family amino acid metabolic process oxoacid metabolic process pyruvate family amino acid biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process branched-chain amino acid metabolic process L-leucine metabolic process L-leucine biosynthetic process organonitrogen compound metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process branched-chain amino acid biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process pollen development	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle plastid stroma chloroplast stroma chloroplast cytosol chloroplast envelope organelle envelope membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle plastid stroma chloroplast stroma chloroplast cytosol chloroplast envelope organelle envelope plastid envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004429	Isopropylmalate dehydrogenase	Family
A, B, C, D	IPR024084	Isopropylmalate dehydrogenase-like domain	Domain
A, B, C, D	IPR019818	Isocitrate/isopropylmalate dehydrogenase, conserved site	Conserved Site

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.