2EQ8 | pdb_00002eq8

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdp

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8076215	3001183	SCOP2B (2022-06-29)
C	SCOP2 Family	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8076214	4000730	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8076215	3001183	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Amino_oxidase	e2eq8A4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Amino_oxidase	ECOD (v294.1)
B	Amino_oxidase	e2eq8B4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Amino_oxidase	ECOD (v294.1)
D	Amino_oxidase	e2eq8D4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Amino_oxidase	ECOD (v294.1)
E	Pyr_redox_dim	e2eq8E4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Pyr_redox_dim	ECOD (v294.1)
E	Amino_oxidase	e2eq8E5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Amino_oxidase	ECOD (v294.1)
F	Me-amine-dh_H	e2eq8F1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Me-amine-dh_H	ECOD (v294.1)
C	E3_binding	e2eq8C1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: E3_binding	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, D, E	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, D, E	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
C, 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, D, E	Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component	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	2-oxoglutarate metabolic process oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process	-
C, F	Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component	fatty acid binding organic acid binding binding ion binding anion binding lipid binding lipoic acid binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding acetyltransferase activity catalytic activity, acting on a protein fatty acid binding organic acid binding binding ion binding anion binding lipid binding lipoic acid binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding 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	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

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

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.