5GUW

Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa

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: OPM
Membrane Protein Annotation: PDBTM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth M]	SCOP2B Superfamily	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	8042871	3001509	SCOP2B (2022-06-29)
E [auth M]	SCOP2B Superfamily	Cytochrome c	8036498	3000815	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	8042871	3001509	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	Cytochrome c	8036498	3000815	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	NorB	e5guwA1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: NorB	ECOD (1.6)
C	NorB	e5guwC1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: NorB	ECOD (1.6)
B	COX1_1	e5guwB1	A: alpha superhelices	X: Cytochrome c oxidase subunit I-like	H: Cytochrome c oxidase subunit I-like (From Topology)	T: Cytochrome c oxidase subunit I-like	F: COX1_1	ECOD (1.6)
D	COX1_1	e5guwD1	A: alpha superhelices	X: Cytochrome c oxidase subunit I-like	H: Cytochrome c oxidase subunit I-like (From Topology)	T: Cytochrome c oxidase subunit I-like	F: COX1_1	ECOD (1.6)
E [auth M]	Cytochrom_D1	e5guwM2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: Cytochrom_D1	ECOD (1.6)
E [auth M]	Cytochrome_CBB3	e5guwM1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
F [auth N]	Cytochrom_D1	e5guwN2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: Cytochrom_D1	ECOD (1.6)
F [auth N]	Cytochrome_CBB3	e5guwN1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
C	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
B	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
D	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
E [auth M]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
E [auth M]	2.140.10.20	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
F [auth N]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
F [auth N]	2.140.10.20	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00034	Cytochrome c (Cytochrom_C)	Cytochrome c	The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family.	Domain
B, D	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family
E [auth M], F [auth N]	PF02239	Cytochrome D1 heme domain (Cytochrom_D1)	Cytochrome D1 heme domain	-	Repeat
E [auth M], F [auth N]	PF13442	Cytochrome C oxidase, cbb3-type, subunit III (Cytochrome_CBB3)	Cytochrome C oxidase, cbb3-type, subunit III	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Nitric oxide reductase subunit C	binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	cell periphery cellular anatomical structure plasma membrane membrane
B, D	Nitric oxide reductase subunit B	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 oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity 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 oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor oxidoreductase activity, acting on other nitrogenous compounds as donors nitric oxide reductase activity cation binding ion binding metal ion binding small molecule binding	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy nitrogen cycle metabolic process denitrification pathway respiratory electron transport chain electron transport chain	cell periphery cellular anatomical structure plasma membrane membrane
E [auth M], F [auth N]	Nitrite reductase	hydroxylamine reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor nitrite reductase (NO-forming) activity nitrite reductase activity electron transfer activity cation binding ion binding hydroxylamine reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor nitrite reductase (NO-forming) activity nitrite reductase activity electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
A, C	IPR009056	Cytochrome c-like domain	Domain
B, D	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
B, D	IPR000883	Cytochrome c oxidase subunit I	Family
B, D	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
B, D	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
E [auth M], F [auth N]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
E [auth M], F [auth N]	IPR011048	Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily	Homologous Superfamily
E [auth M], F [auth N]	IPR009056	Cytochrome c-like domain	Domain
E [auth M], F [auth N]	IPR003143	Cytochrome cd1-nitrite reductase, C-terminal domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E [auth M] A, B, C, D, E [auth M], F [auth N]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex IV (cytochrome c oxidase)	Cytochrome c oxidases

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E [auth M] A, B, C, D, E [auth M], F [auth N]	PDBTM	Annotated as membrane protein by PDBTM

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.