2Q8I

Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol

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)
A	d2q8ia1	All alpha proteins	Bromodomain-like	alpha-ketoacid dehydrogenase kinase, N-terminal domain	alpha-ketoacid dehydrogenase kinase, N-terminal domain	Pyruvate dehydrogenase kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2q8ia3	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	alpha-ketoacid dehydrogenase kinase, C-terminal domain	Pyruvate dehydrogenase kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2q8ib_	All beta proteins	Barrel-sandwich hybrid	Single hybrid motif	Biotinyl/lipoyl-carrier proteins and domains	Lipoyl domain of dihydrolipoamide acetyltransferase	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)
A	SCOP2B Superfamily	alpha-ketoacid dehydrogenase kinase N-terminal domain	8032469	3001773	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GHKL (Gyrase Hsp90 Histidine Kinase MutL) domain-like	8032470	3000091	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Single hybrid motif	8043101	3001880	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	BCDHK_Adom3	e2q8iA1	A: alpha bundles	X: Bromodomain-like	H: alpha-ketoacid dehydrogenase kinase-N (From Topology)	T: alpha-ketoacid dehydrogenase kinase-N	F: BCDHK_Adom3	ECOD (1.6)
A	HATPase_c	e2q8iA2	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c	ECOD (1.6)
B	Biotin_lipoyl	e2q8iB1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.140.20	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
A	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
B	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02518	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (HATPase_c)	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.	Domain
A	PF10436	Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase (BCDHK_Adom3)	Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase	-	Family
B	PF00364	Biotin-requiring enzyme (Biotin_lipoyl)	Biotin-requiring enzyme	This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognise the Glycine cleavage system H proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyruvate dehydrogenase (acetyl-transferring) 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 protein serine/threonine kinase activity	cellular response to stimulus regulation of biological process regulation of cellular process intracellular receptor signaling pathway response to stimulus signaling biological regulation cell communication peroxisome proliferator activated receptor signaling pathway cellular process signal transduction organonitrogen compound metabolic process protein phosphorylation phosphorylation cellular response to stimulus regulation of biological process regulation of cellular process intracellular receptor signaling pathway response to stimulus signaling biological regulation cell communication peroxisome proliferator activated receptor signaling pathway cellular process signal transduction organonitrogen compound metabolic process protein phosphorylation phosphorylation cellular metabolic process primary metabolic process peptidyl-serine modification organic substance metabolic process peptidyl-serine phosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process response to organic substance homeostatic process response to monosaccharide response to carbohydrate carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus cellular response to organic substance response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus cellular homeostasis chemical homeostasis response to glucose response to chemical glucose homeostasis response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to stress response to hypoxia response to stress hypoxia-inducible factor-1alpha signaling pathway response to oxygen levels response to abiotic stimulus nucleoside bisphosphate metabolic process ribonucleoside bisphosphate biosynthetic process regulation of acyl-CoA biosynthetic process regulation of amide metabolic process oxoacid metabolic process nucleotide biosynthetic process regulation of lipid metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process acetyl-CoA metabolic process organic acid metabolic process regulation of nucleotide biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process cellular ketone metabolic process regulation of sulfur metabolic process regulation of small molecule metabolic process regulation of nucleotide metabolic process regulation of phosphate metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process thioester metabolic process regulation of nucleobase-containing compound metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process pyruvate metabolic process regulation of cellular ketone metabolic process amide biosynthetic process regulation of cellular metabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process organic cyclic compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process regulation of fatty acid metabolic process cellular lipid metabolic process regulation of phosphorus metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process regulation of metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process purine nucleoside bisphosphate metabolic process ribonucleoside bisphosphate metabolic process acetyl-CoA biosynthetic process from pyruvate thioester biosynthetic process cellular biosynthetic process purine nucleotide metabolic process acyl-CoA metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process purine nucleoside bisphosphate biosynthetic process regulation of acetyl-CoA biosynthetic process from pyruvate amide metabolic process carbohydrate derivative biosynthetic process regulation of biosynthetic process regulation of purine nucleotide biosynthetic process fatty acid metabolic process nucleoside bisphosphate biosynthetic process carboxylic acid metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process regulation of cellular biosynthetic process acetyl-CoA biosynthetic process organophosphate metabolic process lipid metabolic process response to lipid response to fatty acid cellular response to fatty acid cellular response to lipid reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle mitochondrial matrix
B	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex	acetyltransferase activity catalytic activity, acting on a protein acyltransferase activity dihydrolipoyllysine-residue acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity S-acetyltransferase activity S-acyltransferase activity catalytic activity identical protein binding protein binding binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process primary metabolic process generation of precursor metabolites and energy nucleoside bisphosphate metabolic process ribonucleoside bisphosphate biosynthetic process oxoacid metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process primary metabolic process generation of precursor metabolites and energy nucleoside bisphosphate metabolic process ribonucleoside bisphosphate biosynthetic process oxoacid metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process acetyl-CoA metabolic process organic acid metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process thioester metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process pyruvate metabolic process amide biosynthetic process nucleotide metabolic process organic cyclic compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process purine nucleoside bisphosphate metabolic process ribonucleoside bisphosphate metabolic process acetyl-CoA biosynthetic process from pyruvate thioester biosynthetic process cellular biosynthetic process purine nucleotide metabolic process organic substance metabolic process acyl-CoA metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process purine nucleoside bisphosphate biosynthetic process amide metabolic process carbohydrate derivative biosynthetic process organonitrogen compound metabolic process nucleoside bisphosphate biosynthetic process carboxylic acid metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process organophosphate metabolic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process glucose metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex pyruvate dehydrogenase complex alpha-ketoacid dehydrogenase complex membrane-enclosed lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex pyruvate dehydrogenase complex alpha-ketoacid dehydrogenase complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003594	Histidine kinase/HSP90-like ATPase	Domain
A	IPR039028	PDK/BCKDK protein kinase	Family
A	IPR036784	Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily	Homologous Superfamily
A	IPR018955	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal	Domain
A	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A	IPR005467	Histidine kinase domain	Domain
B	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain	Domain
B	IPR045257	Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component	Family
B	IPR006257	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex	Family
B	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
B	IPR036625	E3-binding domain superfamily	Homologous Superfamily
B	IPR004167	Peripheral subunit-binding domain	Domain
B	IPR011053	Single hybrid motif	Homologous Superfamily
B	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
B	IPR000089	Biotin/lipoyl attachment	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q15120	Charcot-Marie-Tooth disease Charcot-Marie-Tooth disease X-linked dominant 6 peripheral neuropathy adrenal cortex carcinoma invasive ductal breast carcinoma Mitochondrial Diseases osteosarcoma lung cancer motor peripheral neuropathy pancreatic intraductal papillary-mucinous neoplasm malignant colon neoplasm neurodegenerative disease peripheral nervous system disease
B	Pharos: P10515	pyruvate dehydrogenase E2 deficiency pyruvate dehydrogenase deficiency cirrhosis of liver drug-induced liver injury intellectual disability lung adenocarcinoma Mitochondrial Diseases osteosarcoma Pick disease coronary artery disease hereditary spastic paraplegia large cell medulloblastoma lung cancer myocardial ischemia ovarian cancer pyruvate dehydrogenase E2 deficiency pyruvate dehydrogenase deficiency cirrhosis of liver drug-induced liver injury intellectual disability lung adenocarcinoma Mitochondrial Diseases osteosarcoma Pick disease coronary artery disease hereditary spastic paraplegia large cell medulloblastoma lung cancer myocardial ischemia ovarian cancer dermatomyositis inborn errors of metabolism Leigh syndrome malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm

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.