2Y42 | pdb_00002y42

Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with NADH and Mn

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)
D	d2y42d1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D	d2y42d3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D	d2y42d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d2y42c1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d2y42c3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d2y42c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d2y42b1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d2y42b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d2y42a1	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d2y42a3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d2y42a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8032767	3001375	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8032767	3001375	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8032767	3001375	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8032767	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)
D		e2y42D1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Class I glutamine amidotransferase-like	T: PGM_PMM_II	F:	ECOD (20:10:01)
C		e2y42C1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Class I glutamine amidotransferase-like	T: PGM_PMM_II	F:	ECOD (20:10:01)
B		e2y42B1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Class I glutamine amidotransferase-like	T: PGM_PMM_II	F:	ECOD (20:10:01)
A		e2y42A1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Class I glutamine amidotransferase-like	T: PGM_PMM_II	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
B	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
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	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding NAD binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding NAD binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding 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 identical protein binding protein binding	oxoacid metabolic process pyruvate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process branched-chain amino acid metabolic process L-leucine metabolic process L-leucine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process oxoacid metabolic process pyruvate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process branched-chain amino acid metabolic process L-leucine metabolic process L-leucine biosynthetic process small molecule biosynthetic 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

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.