2PPD | pdb_00002ppd

Oxidized H145A mutant of AfNiR bound to nitric oxide

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)
A	d2ppda2	All beta proteins	Cupredoxin-like	Cupredoxins	Multidomain cupredoxins	Nitrite reductase, NIR, C-terminal domain	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
A	d2ppda1	All beta proteins	Cupredoxin-like	Cupredoxins	Multidomain cupredoxins	Nitrite reductase, NIR, N-terminal domain	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
B	d2ppdb2	All beta proteins	Cupredoxin-like	Cupredoxins	Multidomain cupredoxins	Nitrite reductase, NIR, C-terminal domain	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
B	d2ppdb1	All beta proteins	Cupredoxin-like	Cupredoxins	Multidomain cupredoxins	Nitrite reductase, NIR, N-terminal domain	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
C	d2ppdc2	All beta proteins	Cupredoxin-like	Cupredoxins	Multidomain cupredoxins	Nitrite reductase, NIR, C-terminal domain	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
C	d2ppdc1	All beta proteins	Cupredoxin-like	Cupredoxins	Multidomain cupredoxins	Nitrite reductase, NIR, N-terminal domain	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cupredoxins	8039643	3000886	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cupredoxins	8039642	3000886	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8039642	3000886	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8039643	3000886	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cupredoxins	8039643	3000886	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cupredoxins	8039642	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)
A	Cu-oxidase_2_2	e2ppdA2	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	e2ppdA1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Cu-oxidase_3_1	ECOD (1.6)
B	Cu-oxidase_2_2	e2ppdB2	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	e2ppdB1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Cu-oxidase_3_1	ECOD (1.6)
C	Cu-oxidase_2_2	e2ppdC2	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Cu-oxidase_2_2	ECOD (1.6)
C	Cu-oxidase_3_1	e2ppdC1	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)
A	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)
C	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	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
A, B, C	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A, B, C	IPR008972	Cupredoxin	Homologous Superfamily
A, B, C	IPR001117	Multicopper oxidase, second cupredoxin domain	Domain
A, B, C	IPR001287	Nitrite reductase, copper-type	Family
A, B, C	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.