3DVA

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3dvaa_	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	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
C	d3dvac_	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	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
E	d3dvae_	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	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
G	d3dvag_	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	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d3dvab1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d3dvab2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d3dvad1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d3dvad2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F	d3dvaf1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F	d3dvaf2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
H	d3dvah1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
H	d3dvah2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
I	d3dvai_	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	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
J	d3dvaj_	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	(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	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	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	E1_dh	e3dvaA1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: E1_dh	ECOD (1.6)
C	E1_dh	e3dvaC1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: E1_dh	ECOD (1.6)
E	E1_dh	e3dvaE1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: E1_dh	ECOD (1.6)
G	E1_dh	e3dvaG1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: E1_dh	ECOD (1.6)
B	Transketolase_C	e3dvaB3	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C	ECOD (1.6)
B	Transket_pyr	e3dvaB4	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)
D	Transketolase_C	e3dvaD3	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C	ECOD (1.6)
D	Transket_pyr	e3dvaD4	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)
F	Transketolase_C	e3dvaF1	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C	ECOD (1.6)
F	Transket_pyr	e3dvaF2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)
H	Transketolase_C	e3dvaH1	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C	ECOD (1.6)
H	Transket_pyr	e3dvaH2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)
I	E3_binding	e3dvaI1	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: E3_binding	ECOD (1.6)
J	E3_binding	e3dvaJ1	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: E3_binding	ECOD (1.6)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF00676	Dehydrogenase E1 component (E1_dh)	Dehydrogenase E1 component	-	Family
B, D, F, H	PF02779	Transketolase, pyrimidine binding domain (Transket_pyr)	Transketolase, pyrimidine binding domain	This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases.	Domain
B, D, F, H	PF02780	Transketolase, C-terminal domain (Transketolase_C)	Transketolase, C-terminal domain	The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site [2].	Domain
I, J	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, C, E, G	Pyruvate dehydrogenase E1 component subunit alpha	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 pyruvate dehydrogenase activity catalytic activity	-	-
B, D, F, H	Pyruvate dehydrogenase E1 component subunit beta	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 pyruvate dehydrogenase activity catalytic activity	-	-
I, J	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex	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	-	intracellular anatomical structure cytoplasm cellular anatomical entity

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	IPR051467	PDH_E1_beta_subunit	Unknown
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.