3RNM | pdb_00003rnm

The crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2b) bound to human dihydrolipoamide dehydrogenase (E3)

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)
E	d3rnme1	All alpha proteins	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3rnme2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3rnmf1	All alpha proteins	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3rnmf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	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	SCOP2 Family	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8076206	4000730	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8076207	3001183	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8076207	3001183	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)
E	Helicase_C	e3rnmE1	A: a/b three-layered sandwiches	X: Cupredoxin-like	H: Cupredoxin-related	T: Cupredoxin-related	F: Helicase_C	ECOD (v294.1)
F	Radical_SAM	e3rnmF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Radical_SAM	ECOD (v294.1)
B	Radical_SAM	e3rnmB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Radical_SAM	ECOD (v294.1)
C	Radical_SAM	e3rnmC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Radical_SAM	ECOD (v294.1)
D	Radical_SAM	e3rnmD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Radical_SAM	ECOD (v294.1)
A	TetR_N	e3rnmA1	A: a/b three-layered sandwiches	X: Cupredoxin-like	H: Cupredoxin-related	T: Cupredoxin-related	F: TetR_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)
F	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
C	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
C	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
D	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
D	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F	PF02817	e3 binding domain (E3_binding)	e3 binding domain	-	Family
A, B, C, D	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
A, B, C, D	PF02852	Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain (Pyr_redox_dim)	Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial	acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity dihydrolipoamide branched chain acyltransferase activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process small molecule catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process small molecule catabolic process amino acid catabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process fatty-acyl-CoA metabolic process phosphorus metabolic process branched-chain alpha-keto acid decarboxylation to branched-chain acyl-CoA nucleoside phosphate metabolic process purine-containing compound metabolic process fatty acid derivative metabolic process organophosphate metabolic process lipid metabolic process	protein-containing complex catalytic complex branched-chain alpha-ketoacid dehydrogenase complex oxidoreductase complex transferase complex alpha-ketoacid dehydrogenase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex branched-chain alpha-ketoacid dehydrogenase complex oxidoreductase complex transferase complex alpha-ketoacid dehydrogenase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membraneless organelle mitochondrial nucleoid cytoskeleton microtubule cytoskeleton
A, B, C, D	Dihydrolipoyl dehydrogenase, mitochondrial	oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity dihydrolipoyl dehydrogenase (NADH) activity catalytic activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process small molecule catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process small molecule catabolic process amino acid catabolic process developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction gamete generation male gamete generation sperm capacitation anatomical structure maturation cell differentiation anatomical structure development germ cell development cell maturation multicellular organism development multicellular organismal process anatomical structure morphogenesis embryonic morphogenesis embryo development gastrulation nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process fatty-acyl-CoA metabolic process phosphorus metabolic process branched-chain alpha-keto acid decarboxylation to branched-chain acyl-CoA nucleoside phosphate metabolic process purine-containing compound metabolic process fatty acid derivative metabolic process organophosphate metabolic process lipid metabolic process aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, NADH to ubiquinone respiratory electron transport chain mitochondrial ATP synthesis coupled electron transport 2-oxoglutarate metabolic process succinyl-CoA biosynthetic process 2-oxoglutarate decarboxylation to succinyl-CoA purine-containing compound biosynthetic process acyl-CoA biosynthetic process succinyl-CoA metabolic process tricarboxylic acid cycle dicarboxylic acid metabolic process nucleobase-containing compound biosynthetic process sulfur compound biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process biological regulation regulation of biological quality regulation of membrane potential acetyl-CoA metabolic process pyruvate metabolic process pyruvate decarboxylation to acetyl-CoA acetyl-CoA biosynthetic process monocarboxylic acid metabolic process proteolysis protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle acrosomal vesicle acrosomal matrix intracellular vesicle vacuole endomembrane system cytoplasmic vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle acrosomal vesicle acrosomal matrix intracellular vesicle vacuole endomembrane system cytoplasmic vesicle secretory granule secretory vesicle vesicle cell projection cilium motile cilium plasma membrane bounded cell projection protein-containing complex catalytic complex branched-chain alpha-ketoacid dehydrogenase complex oxidoreductase complex transferase complex alpha-ketoacid dehydrogenase complex pyruvate dehydrogenase complex acetyltransferase complex oxoadipate dehydrogenase complex oxoglutarate dehydrogenase complex tricarboxylic acid cycle heteromeric enzyme complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain	Domain
E, F	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
E, F	IPR036625	E3-binding domain superfamily	Homologous Superfamily
E, F	IPR050743	2-oxoacid dehydrogenase family, E2 component	Family
E, F	IPR004167	Peripheral subunit-binding domain	Domain
E, F	IPR011053	Single hybrid motif	Homologous Superfamily
E, F	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
E, F	IPR000089	Biotin/lipoyl attachment	Domain
A, B, C, D	IPR004099	Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain	Domain
A, B, C, D	IPR006258	Dihydrolipoamide dehydrogenase	Family
A, B, C, D	IPR001100	Pyridine nucleotide-disulphide oxidoreductase, class I	Family
A, B, C, D	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily	Homologous Superfamily
A, B, C, D	IPR023753	FAD/NAD(P)-binding domain	Domain
A, B, C, D	IPR050151	Class-I pyridine nucleotide-disulfide oxidoreductase	Family
A, B, C, D	IPR012999	Pyridine nucleotide-disulphide oxidoreductase, class I, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F	Pharos: P11182	maple syrup urine disease malignant ependymoma Maple Syrup Urine Disease, Thiamine Responsive osteosarcoma Pick disease adenoma psoriasis classic maple syrup urine disease esophageal adenocarcinoma glioblastoma inborn errors of metabolism intermediate maple syrup urine disease large cell medulloblastoma malignant glioma medulloblastoma maple syrup urine disease malignant ependymoma Maple Syrup Urine Disease, Thiamine Responsive osteosarcoma Pick disease adenoma psoriasis classic maple syrup urine disease esophageal adenocarcinoma glioblastoma inborn errors of metabolism intermediate maple syrup urine disease large cell medulloblastoma malignant glioma medulloblastoma ovarian cancer plasma cell myeloma astrocytic tumor drug-induced liver injury gastric cancer hepatocellular carcinoma inherited organic acidemia intermittent maple syrup urine disease lung cancer oligodendroglioma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor gastric carcinoma intellectual disability interstitial cystitis
A, B, C, D	Pharos: P09622	maple syrup urine disease pyruvate dehydrogenase E3 deficiency Lactic Acidosis, Congenital Infantile, Due To LAD Deficiency Leigh syndrome cystic fibrosis inflammatory bowel disease plasma cell myeloma ulcerative colitis inherited organic acidemia ovarian cancer pyruvate dehydrogenase deficiency inborn errors of metabolism intellectual disability pancreatic ductal adenocarcinoma

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.