3RNM

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)
B	PF02852	e3rnmB1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: PF02852	ECOD (1.6)
B	PF07992	e3rnmB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF07992	ECOD (1.6)
A	PF02852	e3rnmA1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: PF02852	ECOD (1.6)
A	PF07992	e3rnmA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF07992	ECOD (1.6)
C	PF02852	e3rnmC1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: PF02852	ECOD (1.6)
C	PF07992	e3rnmC3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF07992	ECOD (1.6)
D	PF02852	e3rnmD1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: PF02852	ECOD (1.6)
D	PF07992	e3rnmD3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF07992	ECOD (1.6)
E	PF02817	e3rnmE1	A: alpha arrays	X: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (From Topology)	H: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (From Topology)	T: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	F: PF02817	ECOD (1.6)
F	PF02817	e3rnmF1	A: alpha arrays	X: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (From Topology)	H: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (From Topology)	T: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	F: PF02817	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
E, F	PF02817	e3 binding domain (E3_binding)	e3 binding domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Dihydrolipoyl dehydrogenase, mitochondrial	flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity, acting on a sulfur group of donors dihydrolipoyl dehydrogenase activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor	organonitrogen compound catabolic process catabolic process organonitrogen compound metabolic process oxoacid metabolic process cellular 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 cellular catabolic process organic substance metabolic process carboxylic acid catabolic process organonitrogen compound catabolic process catabolic process organonitrogen compound metabolic process oxoacid metabolic process cellular 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 cellular catabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process branched-chain amino acid metabolic process small molecule catabolic process organic substance 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 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 nucleoside bisphosphate metabolic process ribonucleoside bisphosphate biosynthetic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process acetyl-CoA metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic 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 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 nucleoside bisphosphate biosynthetic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process organophosphate metabolic process biological regulation regulation of biological quality regulation of membrane potential proteolysis protein metabolic process macromolecule 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 transferase complex acetyltransferase complex acrosomal vesicle acrosomal matrix membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex catalytic complex transferase complex acetyltransferase complex 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 oxidoreductase complex pyruvate dehydrogenase complex alpha-ketoacid dehydrogenase complex oxoglutarate dehydrogenase complex tricarboxylic acid cycle heteromeric enzyme complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus
E, F	Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial	acetyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity fatty acid binding organic acid binding binding ion binding organic cyclic compound binding anion binding lipid binding lipoic acid binding carboxylic acid binding acetyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity fatty acid binding organic acid binding binding ion binding organic cyclic compound binding anion binding lipid binding lipoic acid binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity	organonitrogen compound catabolic process catabolic process organonitrogen compound metabolic process oxoacid metabolic process cellular 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 cellular catabolic process organic substance metabolic process carboxylic acid catabolic process organonitrogen compound catabolic process catabolic process organonitrogen compound metabolic process oxoacid metabolic process cellular 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 cellular catabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process branched-chain amino acid metabolic process small molecule catabolic process organic substance catabolic process amino acid catabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle mitochondrial nucleoid non-membrane-bounded organelle cytoskeleton microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR012999	Pyridine nucleotide-disulphide oxidoreductase, class I, active site	Active Site
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	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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
E, F	Pharos: P11182	maple syrup urine disease malignant ependymoma Maple Syrup Urine Disease, Thiamine Responsive osteosarcoma adenoma Pick disease classic maple syrup urine disease psoriasis 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 adenoma Pick disease classic maple syrup urine disease psoriasis esophageal adenocarcinoma glioblastoma inborn errors of metabolism intermediate maple syrup urine disease large cell medulloblastoma malignant glioma medulloblastoma ovarian cancer astrocytic tumor plasma cell myeloma drug-induced liver injury gastric cancer hepatocellular carcinoma inherited organic acidemia intermittent maple syrup urine disease lung cancer oligodendroglioma pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor primitive neuroectodermal tumor gastric carcinoma intellectual disability interstitial cystitis

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 R01GM133198.