2F5Z | pdb_00002f5z

Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
K	EF-hand_6	e2f5zK1	A: a/b three-layered sandwiches	X: Globin-like	H: Globin-like	T: Globin-like	F: EF-hand_6	ECOD (v294.1)
L	MATH_2	e2f5zL1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
M	MATH_2	e2f5zM1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
N	MATH_2	e2f5zN1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
O	MATH_2	e2f5zO1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
A	EF-hand_6	e2f5zA1	A: a/b three-layered sandwiches	X: Globin-like	H: Globin-like	T: Globin-like	F: EF-hand_6	ECOD (v294.1)
B	MATH_2	e2f5zB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
C	MATH_2	e2f5zC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
D	MATH_2	e2f5zD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
E	MATH_2	e2f5zE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
F	MATH_2	e2f5zF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
G	MATH_2	e2f5zG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
H	MATH_2	e2f5zH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
I	MATH_2	e2f5zI1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
J	MATH_2	e2f5zJ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)
L	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)
M	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)
N	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)
O	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	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)
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)
E	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
E	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
F	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
F	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
G	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
G	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
H	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
H	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
I	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
I	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
J	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
J	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
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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, E A, B, C, D, E, F, G, H, I, J	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
K, L, M, N, O	Pyruvate dehydrogenase protein X component	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	aerobic respiration cellular respiration energy derivation by oxidation of organic compounds 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 aerobic respiration cellular respiration energy derivation by oxidation of organic compounds 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 primary metabolic process generation of precursor metabolites and energy 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 metabolic process cellular process monocarboxylic acid 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 cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen mitochondrial matrix
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	Dihydrolipoyl dehydrogenase	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
K, L, M, N, O	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain	Domain
K, L, M, N, O	IPR045257	Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component	Family
K, L, M, N, O	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
K, L, M, N, O	IPR036625	E3-binding domain superfamily	Homologous Superfamily
K, L, M, N, O	IPR004167	Peripheral subunit-binding domain	Domain
K, L, M, N, O	IPR011053	Single hybrid motif	Homologous Superfamily
K, L, M, N, O	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
K, L, M, N, O	IPR000089	Biotin/lipoyl attachment	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR004099	Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR006258	Dihydrolipoamide dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR001100	Pyridine nucleotide-disulphide oxidoreductase, class I	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR023753	FAD/NAD(P)-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR050151	Class-I pyridine nucleotide-disulfide oxidoreductase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR012999	Pyridine nucleotide-disulphide oxidoreductase, class I, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
K, L, M, N, O	Pharos: O00330	pyruvate dehydrogenase E3-binding protein deficiency intellectual disability pyruvate dehydrogenase deficiency Epileptic encephalopathy inborn errors of metabolism lung disease psoriasis systemic lupus erythematosus hereditary spastic paraplegia ovarian cancer uterine corpus leiomyoma IgA glomerulonephritis Leigh syndrome
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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