3D2R | pdb_00003d2r

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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	SH2	e3d2rB3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: SH2	ECOD (develop294)
A	SH2	e3d2rA3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: SH2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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	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 protein serine/threonine kinase activity 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	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation regulation of biological process regulation of cellular process ketone metabolic process biological regulation metabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation regulation of biological process regulation of cellular process ketone metabolic process biological regulation metabolic process regulation of metabolic process regulation of ketone metabolic process oxoacid metabolic 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 regulation of small molecule metabolic process small molecule metabolic process regulation of biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process fatty acid biosynthetic process biosynthetic process regulation of fatty acid biosynthetic process regulation of fatty acid metabolic process regulation of lipid biosynthetic process monocarboxylic acid 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 chemical homeostasis homeostatic process regulation of pH monoatomic ion homeostasis monoatomic cation homeostasis aerobic respiration regulation of acyl-CoA biosynthetic process acetyl-CoA metabolic process nucleobase-containing compound metabolic process regulation of sulfur metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process nucleoside phosphate metabolic process pyruvate metabolic process pyruvate decarboxylation to acetyl-CoA sulfur compound biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process regulation of phosphorus metabolic process cellular respiration energy derivation by oxidation of organic compounds acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process regulation of pyruvate decarboxylation to acetyl-CoA generation of precursor metabolites and energy nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process organophosphate metabolic process regulation of fatty acid oxidation fatty acid oxidation lipid oxidation lipid modification response to lipid response to fatty acid cellular response to fatty acid cellular response to lipid 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 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm 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	IPR018955	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal	Domain
A, B	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B	IPR003594	Histidine kinase/HSP90-like ATPase domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.