3D2R

Crystal structure of pyruvate dehydrogenase kinase isoform 4 in complex with ADP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d3d2ra1	All alpha proteins	Bromodomain-like	alpha-ketoacid dehydrogenase kinase, N-terminal domain	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3d2ra2	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	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3d2rb1	All alpha proteins	Bromodomain-like	alpha-ketoacid dehydrogenase kinase, N-terminal domain	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3d2rb2	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	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	BCDHK_Adom3	e3d2rA4	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	e3d2rA3	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	BCDHK_Adom3	e3d2rB4	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)
B	HATPase_c	e3d2rB3	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)

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	1.20.140.20	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
B	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	PF10436	Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase (BCDHK_Adom3)	Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4	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 binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate 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 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	cellular metabolic process reactive oxygen species metabolic process metabolic process cellular process chemical homeostasis homeostatic process regulation of pH biological regulation monoatomic ion homeostasis monoatomic cation homeostasis regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process cellular metabolic process reactive oxygen species metabolic process metabolic process cellular process chemical homeostasis homeostatic process regulation of pH biological regulation monoatomic ion homeostasis monoatomic cation homeostasis regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process regulation of anoikis negative regulation of biological process regulation of programmed cell death cell death negative regulation of anoikis negative regulation of apoptotic process anoikis negative regulation of cellular process apoptotic process programmed cell death multicellular organismal process regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis regulation of multicellular organismal process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation oxoacid metabolic process cellular biosynthetic process regulation of lipid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process cellular ketone metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of biosynthetic process fatty acid metabolic process regulation of cellular ketone metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process regulation of cellular metabolic process fatty acid biosynthetic process regulation of cellular biosynthetic process biosynthetic process regulation of fatty acid biosynthetic process cellular lipid metabolic process regulation of fatty acid metabolic process regulation of lipid biosynthetic process monocarboxylic acid metabolic process regulation of metabolic process lipid metabolic process cellular response to nitrogen compound signaling response to peptide hormone insulin receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular response to endogenous stimulus response to hormone signal transduction enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus cell surface receptor signaling pathway response to endogenous stimulus response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical response to insulin cellular response to insulin stimulus regulation of fatty acid oxidation fatty acid oxidation lipid oxidation lipid modification regulation of acyl-CoA biosynthetic process regulation of amide metabolic process acetyl-CoA metabolic process nucleobase-containing compound metabolic process regulation of sulfur metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process thioester metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process nucleoside phosphate metabolic process pyruvate metabolic process amide biosynthetic process sulfur compound biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process regulation of phosphorus metabolic process acetyl-CoA biosynthetic process from pyruvate thioester biosynthetic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process regulation of acetyl-CoA biosynthetic process from pyruvate amide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process organophosphate metabolic process response to lipid response to fatty acid cellular response to fatty acid cellular response to lipid monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process glucose homeostasis carbohydrate homeostasis	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR039028	PDK/BCKDK protein kinase	Family
A, B	IPR036784	Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A, B	IPR018955	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal	Domain
A, B	IPR005467	Histidine kinase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q16654	Diabetes Mellitus, Experimental tuberculosis gastric cancer invasive ductal breast carcinoma malignant colon neoplasm breast cancer malignant pancreatic neoplasm Crohn disease non-small cell lung carcinoma Down syndrome pancreatic ductal adenocarcinoma drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sinusitis endometriosis Diabetes Mellitus, Experimental tuberculosis gastric cancer invasive ductal breast carcinoma malignant colon neoplasm breast cancer malignant pancreatic neoplasm Crohn disease non-small cell lung carcinoma Down syndrome pancreatic ductal adenocarcinoma drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sinusitis endometriosis ulcerative colitis gastric carcinoma juvenile dermatomyositis lung adenocarcinoma atopic eczema malignant ependymoma breast carcinoma MALT lymphoma myocardial ischemia cystic fibrosis osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer ductal breast carcinoma in situ exocrine pancreatic carcinoma glioblastoma hepatocellular carcinoma large cell medulloblastoma lung cancer atypical teratoid rhabdoid tumor malignant glioma breast fibroadenoma medulloblastoma coronary artery disease myopathy ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis Emery-Dreifuss muscular dystrophy

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.