2VPY

Polysulfide reductase with bound quinone inhibitor, pentachlorophenol (PCP)

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
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	4Fe-4S ferredoxins	8087201	3000020	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	4Fe-4S ferredoxins	8087201	3000020	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)
B	Fer4_11	e2vpyB1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11	ECOD (1.6)
B	Fer4_11_1	e2vpyB2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11_1	ECOD (1.6)
E [auth F]	Fer4_11	e2vpyF1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11	ECOD (1.6)
E [auth F]	Fer4_11_1	e2vpyF2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11_1	ECOD (1.6)
C	NrfD_2_C	e2vpyC2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: NrfD_2_C	ECOD (1.6)
C	NrfD_2	e2vpyC1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: NrfD_2	ECOD (1.6)
F [auth G]	NrfD_2_C	e2vpyG2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: NrfD_2_C	ECOD (1.6)
F [auth G]	NrfD_2	e2vpyG1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: NrfD_2	ECOD (1.6)
A	Molydop_binding	e2vpyA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
A	Molybdop_Fe4S4	e2vpyA3	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4	ECOD (1.6)
A	Molybdopterin_2nd	e2vpyA4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
A	Molybdopterin_1st_1	e2vpyA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
D [auth E]	Molydop_binding	e2vpyE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
D [auth E]	Molybdop_Fe4S4	e2vpyE3	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4	ECOD (1.6)
D [auth E]	Molybdopterin_2nd	e2vpyE4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
D [auth E]	Molybdopterin_1st_1	e2vpyE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
E [auth F]	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	1.20.1630.10	Mainly Alpha	Up-down Bundle	Formate dehydrogenase/DMSO reductase fold	Formate dehydrogenase/DMSO reductase domain	CATH (4.3.0)
F [auth G]	1.20.1630.10	Mainly Alpha	Up-down Bundle	Formate dehydrogenase/DMSO reductase fold	Formate dehydrogenase/DMSO reductase domain	CATH (4.3.0)
A	2.20.25.90	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	ADC-like domains	CATH (4.3.0)
A	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
A	3.30.2070.10	Alpha Beta	2-Layer Sandwich	Formate dehydrogenase/DMSO reductase,	Formate dehydrogenase/DMSO reductase,	CATH (4.3.0)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
D [auth E]	2.20.25.90	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	ADC-like domains	CATH (4.3.0)
D [auth E]	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D [auth E]	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
D [auth E]	3.30.2070.10	Alpha Beta	2-Layer Sandwich	Formate dehydrogenase/DMSO reductase,	Formate dehydrogenase/DMSO reductase,	CATH (4.3.0)
D [auth E]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E [auth F]	PF13247	4Fe-4S dicluster domain (Fer4_11)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
B, E [auth F]	PF12800	4Fe-4S binding domain (Fer4_4)	4Fe-4S binding domain	This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich.	Domain
A, D [auth E]	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entir ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
A, D [auth E]	PF04879	Molybdopterin oxidoreductase Fe4S4 domain (Molybdop_Fe4S4)	Molybdopterin oxidoreductase Fe4S4 domain	This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1].	Domain
A, D [auth E]	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E [auth F]	NRFC PROTEIN	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding metal ion binding	-	-
C, F [auth G]	HYPOTHETICAL MEMBRANE SPANNING PROTEIN	-	-	cellular anatomical structure membrane
A, D [auth E]	THIOSULFATE REDUCTASE	oxidoreductase activity catalytic activity binding organic cyclic compound binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E [auth F]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, E [auth F]	IPR050954	Electron Transfer Iron-Sulfur Cluster-Binding Protein	Family
B, E [auth F]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, E [auth F]	IPR000813	7Fe ferredoxin	Family
C, F [auth G]	IPR032796	Polysulfide reductase	Family
A, D [auth E]	IPR050612	Prokaryotic Molybdopterin Oxidoreductases	Family
A, D [auth E]	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A, D [auth E]	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A, D [auth E]	IPR006656	Molybdopterin oxidoreductase	Domain
A, D [auth E]	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A, D [auth E]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, D [auth E]	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
C, F [auth G]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
C, F [auth G]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Mo/Wbis-MGD Oxidoreductases	Polysulfide Reductase PsrABC (native)

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.