2PNR | pdb_00002pnr

Crystal Structure of the asymmetric Pdk3-l2 Complex

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)
F [auth G]	d2pnrg_	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)
C	d2pnrc_	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)
E [auth F]	d2pnrf1	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)
E [auth F]	d2pnrf2	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)
D [auth E]	d2pnre1	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)
D [auth E]	d2pnre3	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	d2pnrb1	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)
B	d2pnrb2	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)
A	d2pnra1	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	d2pnra3	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth F]	SCOP2B Superfamily	alpha-ketoacid dehydrogenase kinase, N-terminal domain	8032469	3001773	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8032470	3000091	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	alpha-ketoacid dehydrogenase kinase, N-terminal domain	8032469	3001773	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8032470	3000091	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8032470	3000091	SCOP2B (2022-06-29)
B	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)
A	SCOP2B Superfamily	alpha-ketoacid dehydrogenase kinase, N-terminal domain	8032469	3001773	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)
F [auth G]		e2pnrG1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: TPR_COPA_B	F:	ECOD (20:10:01)
C		e2pnrC1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: Histone	F:	ECOD (20:10:01)
E [auth F]		e2pnrF3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: SH2	F:	ECOD (20:10:01)
D [auth E]		e2pnrE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
D [auth E]		e2pnrE2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
B		e2pnrB3	A: HTH	X: HTH	H: winged helix domain	T: PI3K_C2	F:	ECOD (20:10:01)
A		e2pnrA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
A		e2pnrA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth G]	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)
C	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)
E [auth F]	1.20.140.20	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
E [auth F]	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
D [auth E]	1.20.140.20	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
D [auth E]	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)
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, D [auth E], E [auth F]	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, D [auth E], E [auth F]	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
C, F [auth G]	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 primary metabolic process metabolic process cellular process generation of precursor metabolites and energy oxoacid metabolic process acetyl-CoA metabolic process organic acid metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule 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 oxoacid metabolic process acetyl-CoA metabolic process organic acid metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process pyruvate metabolic process carboxylic acid metabolic process pyruvate decarboxylation to acetyl-CoA nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process monocarboxylic acid metabolic process catabolic process organic acid catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule catabolic process pyruvate catabolic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process glucose metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex transferase complex pyruvate dehydrogenase complex acetyltransferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex transferase complex pyruvate dehydrogenase complex acetyltransferase complex alpha-ketoacid dehydrogenase complex sperm head-tail coupling apparatus membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
A, B, D [auth E], E [auth F]	[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 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 regulation of biological process regulation of cellular process intracellular receptor signaling pathway response to stimulus signaling biological regulation intracellular signal transduction cell communication peroxisome proliferator activated receptor signaling pathway cellular process signal transduction nuclear receptor-mediated signaling pathway aerobic respiration cellular response to stimulus regulation of biological process regulation of cellular process intracellular receptor signaling pathway response to stimulus signaling biological regulation intracellular signal transduction cell communication peroxisome proliferator activated receptor signaling pathway cellular process signal transduction nuclear receptor-mediated signaling pathway aerobic respiration regulation of acyl-CoA biosynthetic process oxoacid metabolic process regulation of lipid metabolic process acetyl-CoA metabolic process organic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of sulfur metabolic process regulation of small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process nucleoside phosphate metabolic process pyruvate metabolic process pyruvate decarboxylation to acetyl-CoA primary metabolic process regulation of ketone metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process regulation of fatty acid metabolic process metabolic process regulation of phosphorus metabolic process monocarboxylic acid metabolic process regulation of metabolic process cellular respiration energy derivation by oxidation of organic compounds ketone metabolic process 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 regulation of biosynthetic process fatty acid metabolic process carboxylic acid metabolic process generation of precursor metabolites and energy nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process organophosphate metabolic process lipid metabolic process protein phosphorylation phosphorylation peptidyl-serine modification peptidyl-serine phosphorylation macromolecule modification peptidyl-amino acid modification protein metabolic process macromolecule metabolic process protein modification process homeostatic process 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 response to monosaccharide response to carbohydrate chemical homeostasis response to glucose response to chemical glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus 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 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F [auth G]	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
A, B, D [auth E], E [auth F]	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

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.