3LCB | pdb_00003lcb

The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.

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)
C	d3lcbc_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3lcbd_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8034659	3001375	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8034659	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)
C		e3lcbC1	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: Iso_dh	F:	ECOD (20:10:01)
D		e3lcbD1	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: Iso_dh	F:	ECOD (20:10:01)
A		e3lcbA1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Tachylectin	F:	ECOD (20:10:01)
B		e3lcbB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Tachylectin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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
C, D	PF00180	Isocitrate/isopropylmalate dehydrogenase (Iso_dh)	Isocitrate/isopropylmalate dehydrogenase		Domain
A, B	PF06315	Isocitrate dehydrogenase kinase/phosphatase (AceK) kinase domain (AceK_kinase)	Isocitrate dehydrogenase kinase/phosphatase (AceK) kinase domain	This the C-terminal protein kinase domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (EC:2.7.1.116) [1,2]. It has a classic bi-lobe protein kinase fold with the ATP-binding cleft located at the interface between the two ...	This the C-terminal protein kinase domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (EC:2.7.1.116) [1,2]. It has a classic bi-lobe protein kinase fold with the ATP-binding cleft located at the interface between the two lobes. The N-terminal lobe comprises a twisted antiparallel beta-sheet of five strands and two alpha-helices. The C-terminal lobe is larger and mainly alpha-helical, with some stretches of antiparallel beta-strands [2].	Domain
A, B	PF20423	Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain (AceK_regulatory)	Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain	This is the N-terminal regulatory domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (EC:2.7.1.116) [1,2]. It has an alpha-helical fold, with two long, parallel alpha-helices that form a large hairpin structure followed b ...	This is the N-terminal regulatory domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (EC:2.7.1.116) [1,2]. It has an alpha-helical fold, with two long, parallel alpha-helices that form a large hairpin structure followed by two short, parallel alpha-helices forming a small hairpin segment. This domain is linked to the C-terminal kinase domain by a short (27 residues) alpha-helix [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Isocitrate dehydrogenase [NADP]	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion 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 (NADP+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD binding adenyl nucleotide binding	electron transport chain metabolic process cellular process generation of precursor metabolites and energy aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process electron transport chain metabolic process cellular process generation of precursor metabolites and energy aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process small molecule metabolic process monocarboxylic acid metabolic process response to oxidative stress response to stimulus response to stress	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A, B	Isocitrate dehydrogenase kinase/phosphatase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding AMP binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups [isocitrate dehydrogenase (NADP+)] kinase activity protein serine kinase activity phosphoric ester hydrolase activity phosphoprotein phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase 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 carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic 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 glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process small molecule metabolic process monocarboxylic acid metabolic process monosaccharide metabolic process hexose metabolic process glucose metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR004439	Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic	Family
C, D	IPR024084	Isopropylmalate dehydrogenase-like domain	Domain
C, D	IPR019818	Isocitrate/isopropylmalate dehydrogenase, conserved site	Conserved Site
A, B	IPR046854	Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain	Domain
A, B	IPR046855	Isocitrate dehydrogenase kinase/phosphatase (AceK), kinase domain	Domain
A, B	IPR010452	Isocitrate dehydrogenase kinasephosphatase	Family

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.