1W88 | pdb_00001w88

The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1w88a_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	Pyruvate dehydrogenase E1-alpha, PdhA	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
C	d1w88c_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	Pyruvate dehydrogenase E1-alpha, PdhA	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
E	d1w88e_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	Pyruvate dehydrogenase E1-alpha, PdhA	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
G	d1w88g_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	Pyruvate dehydrogenase E1-alpha, PdhA	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d1w88b1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d1w88b2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d1w88d1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d1w88d2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F	d1w88f1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F	d1w88f2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
H	d1w88h1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
H	d1w88h2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
I	d1w88i_	All alpha proteins	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	E3/E1 binding domain of dihydrolipoyl acetyltransferase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
J	d1w88j_	All alpha proteins	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	E3/E1 binding domain of dihydrolipoyl acetyltransferase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8043331	3001183	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8043331	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)
A	Esterase	e1w88A1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Esterase	ECOD (develop294)
C	Esterase	e1w88C1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Esterase	ECOD (develop294)
E	Esterase	e1w88E1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Esterase	ECOD (develop294)
G	Esterase	e1w88G1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Esterase	ECOD (develop294)
B	Pribosyltran	e1w88B1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
B	E1_dh	e1w88B2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (develop294)
D	Pribosyltran	e1w88D1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
D	E1_dh	e1w88D2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (develop294)
F	Pribosyltran	e1w88F1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
F	E1_dh	e1w88F2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (develop294)
H	Pribosyltran	e1w88H1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
H	E1_dh	e1w88H2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (develop294)
I	EF-hand_1,S_100	e1w88I1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: EF-hand_1,S_100	ECOD (develop294)
J	EF-hand_1,S_100	e1w88J1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: EF-hand_1,S_100	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
C	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
E	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
G	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
B	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
B	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
D	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
F	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
F	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
H	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
H	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
I	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)
J	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor oxidoreductase activity pyruvate dehydrogenase (acetyl-transferring) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity	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	-
B, D, F, H	PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor oxidoreductase activity pyruvate dehydrogenase (acetyl-transferring) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity	-	-
I, J	DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE	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	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR017596	Pyruvate dehydrogenase E1 component subunit alpha/BCKADH E1-alpha	Family
A, C, E, G	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, C, E, G	IPR050771	Alpha-ketoacid dehydrogenase complex E1 component	Family
A, C, E, G	IPR001017	Dehydrogenase, E1 component	Domain
B, D, F, H	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
B, D, F, H	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
B, D, F, H	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
B, D, F, H	IPR033248	Transketolase, C-terminal domain	Domain
I, J	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain	Domain
I, J	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
I, J	IPR036625	E3-binding domain superfamily	Homologous Superfamily
I, J	IPR050743	2-oxoacid dehydrogenase family, E2 component	Family
I, J	IPR004167	Peripheral subunit-binding domain	Domain
I, J	IPR011053	Single hybrid motif	Homologous Superfamily
I, J	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
I, J	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.