2PDA | pdb_00002pda

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS AND PYRUVATE.

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	d2pdaa1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	PFOR Pyr module	Pyruvate-ferredoxin oxidoreductase, PFOR, domain I	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
A	d2pdaa2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	PFOR PP module	Pyruvate-ferredoxin oxidoreductase, PFOR, domains VI	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
A	d2pdaa3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Pyruvate-ferredoxin oxidoreductase, PFOR, domain II	Pyruvate-ferredoxin oxidoreductase, PFOR, domain II	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
A	d2pdaa4	Alpha and beta proteins (a/b)	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
A	d2pdaa5	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2pdab1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	PFOR Pyr module	Pyruvate-ferredoxin oxidoreductase, PFOR, domain I	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2pdab2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	PFOR PP module	Pyruvate-ferredoxin oxidoreductase, PFOR, domains VI	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2pdab3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Pyruvate-ferredoxin oxidoreductase, PFOR, domain II	Pyruvate-ferredoxin oxidoreductase, PFOR, domain II	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2pdab4	Alpha and beta proteins (a/b)	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2pdab5	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	8039282	3000879	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	4Fe-4S ferredoxins	8039286	3000020	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8039273	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TK C-terminal domain-like	8039278	3000424	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8039276	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TK C-terminal domain-like	8039278	3000424	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8039276	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	4Fe-4S ferredoxins	8039286	3000020	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8039273	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	8039282	3000879	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	pyruv_ox_red	e2pdaA6	A: alpha bundles	X: Bromodomain-like	H: Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase (From Topology)	T: Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase	F: pyruv_ox_red	ECOD (1.6)
A	Fer4_21_1	e2pdaA1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
A	POR	e2pdaA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	F: POR	ECOD (1.6)
A	Transketolase_C	e2pdaA2	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)
A	POR_N	e2pdaA4	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: POR_N	ECOD (1.6)
A	TPP_enzyme_C	e2pdaA5	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: TPP_enzyme_C	ECOD (1.6)
B	pyruv_ox_red	e2pdaB5	A: alpha bundles	X: Bromodomain-like	H: Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase (From Topology)	T: Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase	F: pyruv_ox_red	ECOD (1.6)
B	Fer4_21_1	e2pdaB1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
B	POR	e2pdaB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	F: POR	ECOD (1.6)
B	Transketolase_C	e2pdaB2	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	POR_N	e2pdaB4	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: POR_N	ECOD (1.6)
B	TPP_enzyme_C	e2pdaB6	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: TPP_enzyme_C	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 (4.2.0)
A	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.2.0)
A	3.40.920.10	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate-ferredoxin Oxidoreductase	domain 3	CATH (4.2.0)
A	4.10.780.10	Few Secondary Structures	Irregular	Pyruvate-ferredoxin Oxidoreductase	domain 4	CATH (4.2.0)
A	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.2.0)
A	4.10.790.10	Few Secondary Structures	Irregular	Pyruvate-ferredoxin Oxidoreductase	domain 7	CATH (4.2.0)
B	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.2.0)
B	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.2.0)
B	3.40.920.10	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate-ferredoxin Oxidoreductase	domain 3	CATH (4.2.0)
B	4.10.780.10	Few Secondary Structures	Irregular	Pyruvate-ferredoxin Oxidoreductase	domain 4	CATH (4.2.0)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.2.0)
B	4.10.790.10	Few Secondary Structures	Irregular	Pyruvate-ferredoxin Oxidoreductase	domain 7	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)	cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding pyruvate synthase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding pyruvate synthase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding vitamin binding thiamine pyrophosphate binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	electron transport chain metabolic process cellular process generation of precursor metabolites and energy response to oxidative stress response to stimulus response to stress	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR055168	Pyruvate-ferredoxin oxidoreductase, insertion domain	Domain
A, B	IPR011895	Pyruvate-flavodoxin oxidoreductase	Family
A, B	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
A, B	IPR019752	Pyruvate/ketoisovalerate oxidoreductase, catalytic domain	Domain
A, B	IPR050722	Pyruvate:ferredoxin/flavodoxin oxidoreductase	Family
A, B	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, B	IPR002869	Pyruvate-flavodoxin oxidoreductase, central domain	Homologous Superfamily
A, B	IPR033412	Pyruvate:ferredoxin oxidoreductase, core domain II	Domain
A, B	IPR019456	Pyruvate-flavodoxin oxidoreductase, EKR domain	Domain
A, B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, B	IPR037112	Pyruvate-flavodoxin oxidoreductase, EKR domain superfamily	Homologous Superfamily
A, B	IPR002880	Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain	Domain
A, B	IPR011766	Thiamine pyrophosphate enzyme, TPP-binding	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.