3C0D | pdb_00003c0d

Crystal structure of the putative nitrite reductase NADPH (small subunit) oxidoreductase protein Q87HB1. Northeast Structural Genomics Consortium target VpR162

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)
B	d3c0db_	All beta proteins	ISP domain	ISP domain	NirD-like	NADH-nitrite reductase small subunit NirD	(Vibrio parahaemolyticus RIMD 2210633 ) [TaxId: 223926 ],	SCOPe (2.08)
E	d3c0de_	All beta proteins	ISP domain	ISP domain	NirD-like	NADH-nitrite reductase small subunit NirD	(Vibrio parahaemolyticus RIMD 2210633 ) [TaxId: 223926 ],	SCOPe (2.08)
H	d3c0dh_	All beta proteins	ISP domain	ISP domain	NirD-like	NADH-nitrite reductase small subunit NirD	(Vibrio parahaemolyticus RIMD 2210633 ) [TaxId: 223926 ],	SCOPe (2.08)
G	d3c0dg_	All beta proteins	ISP domain	ISP domain	NirD-like	NADH-nitrite reductase small subunit NirD	(Vibrio parahaemolyticus RIMD 2210633 ) [TaxId: 223926 ],	SCOPe (2.08)
F	d3c0df_	All beta proteins	ISP domain	ISP domain	NirD-like	NADH-nitrite reductase small subunit NirD	(Vibrio parahaemolyticus RIMD 2210633 ) [TaxId: 223926 ],	SCOPe (2.08)
D	d3c0dd_	All beta proteins	ISP domain	ISP domain	NirD-like	NADH-nitrite reductase small subunit NirD	(Vibrio parahaemolyticus RIMD 2210633 ) [TaxId: 223926 ],	SCOPe (2.08)
C	d3c0dc_	All beta proteins	ISP domain	ISP domain	NirD-like	NADH-nitrite reductase small subunit NirD	(Vibrio parahaemolyticus RIMD 2210633 ) [TaxId: 223926 ],	SCOPe (2.08)
A	d3c0da1	All beta proteins	ISP domain	ISP domain	NirD-like	NADH-nitrite reductase small subunit NirD	(Vibrio parahaemolyticus RIMD 2210633 ) [TaxId: 223926 ],	SCOPe (2.08)
A	d3c0da2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Vibrio parahaemolyticus RIMD 2210633 ) [TaxId: 223926 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	ISP domain	8039664	3000233	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ISP domain	8039664	3000233	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	ISP domain	8039664	3000233	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	ISP domain	8039664	3000233	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	ISP domain	8039664	3000233	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ISP domain	8039664	3000233	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ISP domain	8039664	3000233	SCOP2B (2022-06-29)
A	SCOP2 Family	NirD-like	8027285	4001733	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ISP domain	8039664	3000233	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)
B	Urease_alpha	e3c0dB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Urease_alpha	ECOD (v294.1)
B	C1_1	e3c0dB2	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
E	Urease_alpha	e3c0dE1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Urease_alpha	ECOD (v294.1)
E	C1_1	e3c0dE2	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
H	Urease_alpha	e3c0dH1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Urease_alpha	ECOD (v294.1)
H	C1_1	e3c0dH2	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
G	Urease_alpha	e3c0dG1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Urease_alpha	ECOD (v294.1)
G	C1_1	e3c0dG2	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
F	Urease_alpha	e3c0dF1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Urease_alpha	ECOD (v294.1)
F	C1_1	e3c0dF2	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
D	Urease_alpha	e3c0dD1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Urease_alpha	ECOD (v294.1)
D	C1_1	e3c0dD2	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
C	Urease_alpha	e3c0dC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Urease_alpha	ECOD (v294.1)
C	C1_1	e3c0dC2	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
A	Rieske_2	e3c0dA1	A: beta sandwiches	X: ISP domain	H: ISP domain	T: ISP domain	F: Rieske_2	ECOD (v294.1)
A	Rieske	e3c0dA2	A: few secondary structure elements	X: Trm112p-like	H: Trm112p-like	T: Trm112p-like	F: Rieske	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
E	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
H	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
G	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
F	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
D	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
C	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
A	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor oxidoreductase activity nitrite reductase [NAD(P)H] activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitrite reductase activity catalytic activity	nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017881	Nitrite reductase (NADH) small subunit	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012748	Rieske-like [2Fe-2S] domain, NirD-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily

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.