5B1J | pdb_00005b1j

Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin

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)
C	d5b1jc_	All beta proteins	Cupredoxin-like	Cupredoxins	automated matches	automated matches	(Hyphomicrobium denitrificans ) [TaxId: 53399 ],	SCOPe (2.08)
B	d5b1jb1	All beta proteins	Cupredoxin-like	Cupredoxins	Multidomain cupredoxins	automated matches	(Achromobacter xylosoxidans ) [TaxId: 85698 ],	SCOPe (2.08)
A	d5b1ja1	All beta proteins	Cupredoxin-like	Cupredoxins	Multidomain cupredoxins	automated matches	(Achromobacter xylosoxidans ) [TaxId: 85698 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Cupredoxins	8068807	3000886	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)
C	Copper-bind	e5b1jC1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Copper-bind	ECOD (1.6)
B	Cu-oxidase_2_2	e5b1jB2	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Cu-oxidase_2_2	ECOD (1.6)
B	Cu-oxidase_3_1	e5b1jB1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Cu-oxidase_3_1	ECOD (1.6)
A	Cu-oxidase_2_2	e5b1jA2	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Cu-oxidase_2_2	ECOD (1.6)
A	Cu-oxidase_3_1	e5b1jA1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Cu-oxidase_3_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	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
C	PF00127	Copper binding proteins, plastocyanin/azurin family (Copper-bind)	Copper binding proteins, plastocyanin/azurin family		Domain
A, B	PF00394	Multicopper oxidase (Cu-oxidase)	Multicopper oxidase	Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.	Domain
A, B	PF07732	Multicopper oxidase (Cu-oxidase_3)	Multicopper oxidase	This entry contains many divergent copper oxidase-like domains that are not recognised by the Pfam:PF00394 model.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Blue copper protein	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding electron transfer activity	-	cellular anatomical structure periplasmic space
A, B	Copper-containing nitrite reductase	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitrite reductase (NO-forming) activity nitrite reductase activity catalytic activity	nitrogen cycle metabolic process denitrification pathway metabolic process cellular process nitrate assimilation oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR002386	Amicyanin/Pseudoazurin	Family
C	IPR012745	Pseudoazurin	Family
C	IPR000923	Blue (type 1) copper domain	Domain
C	IPR008972	Cupredoxin	Homologous Superfamily
C	IPR001235	Blue (type 1) copper protein, plastocyanin-type	Family
A, B	IPR008972	Cupredoxin	Homologous Superfamily
A, B	IPR001117	Multicopper oxidase, second cupredoxin domain	Domain
A, B	IPR045087	Multicopper oxidase	Family
A, B	IPR001287	Nitrite reductase, copper-type	Family
A, B	IPR011707	Multicopper oxidase-like, N-terminal	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.