2RDZ | pdb_00002rdz

High Resolution Crystal Structure of the Escherichia coli Cytochrome c Nitrite Reductase.

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)
D	d2rdzd_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2rdzc_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2rdzb_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2rdza_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	HAO C-terminal domain-like	8056477	3002349	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Di-heme elbow motif	8056476	3000145	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HAO C-terminal domain-like	8056477	3002349	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Di-heme elbow motif	8056476	3000145	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Di-heme elbow motif	8056476	3000145	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAO C-terminal domain-like	8056477	3002349	SCOP2B (2022-06-29)
A	SCOP2 Family	HAO/Nir-like	8056475	4000358	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HAO C-terminal domain-like	8056477	3002349	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Di-heme elbow motif	8056476	3000145	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)
D	Enolase_C	e2rdzD1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Enolase_C	ECOD (develop294)
C	Enolase_C	e2rdzC1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Enolase_C	ECOD (develop294)
B	Enolase_C	e2rdzB1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Enolase_C	ECOD (develop294)
A	Enolase_C	e2rdzA1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Enolase_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
D	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
C	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
C	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
B	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
B	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
A	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
A	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02335	Cytochrome c552 (Cytochrom_C552)	Cytochrome c552	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cytochrome c-552	oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitric oxide reductase activity catalytic activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding nitrite reductase (cytochrome, ammonia-forming) activity nitrite reductase activity tetrapyrrole binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitric oxide reductase activity catalytic activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding nitrite reductase (cytochrome, ammonia-forming) activity nitrite reductase activity tetrapyrrole binding heme binding transition metal ion binding iron ion binding	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 anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain 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 anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain generation of precursor metabolites and energy anaerobic respiration	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017570	Formate-dependent cytochrome c nitrite reductase, c552 subunit	Family
A, B, C, D	IPR036280	Multiheme cytochrome superfamily	Homologous Superfamily
A, B, C, D	IPR003321	Cytochrome c552	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.