1QNI | pdb_00001qni

Crystal Structure of Nitrous Oxide Reductase from Pseudomonas nautica, at 2.4A Resolution

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)
F	d1qnif1	All beta proteins	Cupredoxin-like	Cupredoxins	Nitrosocyanin	Nitrous oxide reductase, C-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
F	d1qnif2	All beta proteins	7-bladed beta-propeller	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
E	d1qnie1	All beta proteins	Cupredoxin-like	Cupredoxins	Nitrosocyanin	Nitrous oxide reductase, C-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
E	d1qnie2	All beta proteins	7-bladed beta-propeller	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
D	d1qnid1	All beta proteins	Cupredoxin-like	Cupredoxins	Nitrosocyanin	Nitrous oxide reductase, C-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
D	d1qnid2	All beta proteins	7-bladed beta-propeller	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
C	d1qnic1	All beta proteins	Cupredoxin-like	Cupredoxins	Nitrosocyanin	Nitrous oxide reductase, C-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
C	d1qnic2	All beta proteins	7-bladed beta-propeller	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
B	d1qnib1	All beta proteins	Cupredoxin-like	Cupredoxins	Nitrosocyanin	Nitrous oxide reductase, C-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
B	d1qnib2	All beta proteins	7-bladed beta-propeller	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
A	d1qnia1	All beta proteins	Cupredoxin-like	Cupredoxins	Nitrosocyanin	Nitrous oxide reductase, C-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)
A	d1qnia2	All beta proteins	7-bladed beta-propeller	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	Nitrous oxide reductase, N-terminal domain	(Marinobacter nauticus ) [TaxId: 2743 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Cupredoxins	8040585	3000886	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nitrous oxide reductase, N-terminal domain	8042848	3001684	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cupredoxins	8040585	3000886	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nitrous oxide reductase, N-terminal domain	8042848	3001684	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cupredoxins	8040585	3000886	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nitrous oxide reductase, N-terminal domain	8042848	3001684	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nitrous oxide reductase, N-terminal domain	8042848	3001684	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cupredoxins	8040585	3000886	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nitrous oxide reductase, N-terminal domain	8042848	3001684	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8040585	3000886	SCOP2B (2022-06-29)
A	SCOP2 Family	Nitrosocyanin	8028206	4002857	SCOP2 (2022-06-29)
A	SCOP2 Family	Nitrous oxide reductase, N-terminal domain	8030469	4002739	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cupredoxins	8040585	3000886	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nitrous oxide reductase, N-terminal domain	8042848	3001684	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)
F	COX2	e1qniF1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
F	PRK02888	e1qniF2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PRK02888	ECOD (1.6)
E	COX2	e1qniE1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
E	PRK02888	e1qniE2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PRK02888	ECOD (1.6)
D	COX2	e1qniD1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
D	PRK02888	e1qniD2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PRK02888	ECOD (1.6)
C	COX2	e1qniC1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
C	PRK02888	e1qniC2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PRK02888	ECOD (1.6)
B	COX2	e1qniB1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
B	PRK02888	e1qniB2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PRK02888	ECOD (1.6)
A	COX2	e1qniA1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
A	PRK02888	e1qniA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PRK02888	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
F	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
E	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
E	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
D	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
D	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
C	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain		Domain
A, B, C, D, E A, B, C, D, E, F	PF18793	Nitrous oxide reductase propeller repeat 2 (nos_propeller_2)	Nitrous oxide reductase propeller repeat 2	-	Repeat
A, B, C, D, E A, B, C, D, E, F	PF18764	Nitrous oxide reductase propeller repeat (nos_propeller)	Nitrous oxide reductase propeller repeat	-	Repeat

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	NITROUS-OXIDE REDUCTASE	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity transition metal ion binding copper ion binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitrous-oxide reductase activity catalytic activity	-	cellular anatomical structure membrane periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR011045	Nitrous oxide reductase, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR023644	Nitrous-oxide reductase	Family
A, B, C, D, E A, B, C, D, E, F	IPR041142	Nitrous oxide reductase, propeller repeat 2	Repeat
A, B, C, D, E A, B, C, D, E, F	IPR034205	Nitrous-oxide reductase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR041114	Nitrous oxide reductase, propeller repeat 1	Repeat
A, B, C, D, E A, B, C, D, E, F	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008972	Cupredoxin	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001505	Copper centre Cu(A)	Binding Site
A, B, C, D, E A, B, C, D, E, F	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR051403	NosZ/Cytochrome c oxidase subunit 2	Family

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.