2J7A | pdb_00002j7a

Crystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
N	d2j7an_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
Q	d2j7aq_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
P	d2j7ap_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
M	d2j7am_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
K	d2j7ak_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
J	d2j7aj_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
H	d2j7ah_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
G	d2j7ag_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
E	d2j7ae_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
D	d2j7ad_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
B	d2j7ab_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
A	d2j7aa_	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Di-heme elbow motif	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
R	Ada_Zn_binding	e2j7aR1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Ada_Zn_binding	ECOD (v294.1)
O	Ada_Zn_binding	e2j7aO1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Ada_Zn_binding	ECOD (v294.1)
L	Ada_Zn_binding	e2j7aL1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Ada_Zn_binding	ECOD (v294.1)
I	Ada_Zn_binding	e2j7aI1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Ada_Zn_binding	ECOD (v294.1)
F	Ada_Zn_binding	e2j7aF1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Ada_Zn_binding	ECOD (v294.1)
C	Ada_Zn_binding	e2j7aC1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Ada_Zn_binding	ECOD (v294.1)
N	Sigma70_r4_2	e2j7aN1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
Q	Sigma70_r4_2	e2j7aQ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
P	Sigma70_r4_2	e2j7aP1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
M	Sigma70_r4_2	e2j7aM1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
K	Sigma70_r4_2	e2j7aK1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
J	Sigma70_r4_2	e2j7aJ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
H	Sigma70_r4_2	e2j7aH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
G	Sigma70_r4_2	e2j7aG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
E	Sigma70_r4_2	e2j7aE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
D	Sigma70_r4_2	e2j7aD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
B	Sigma70_r4_2	e2j7aB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)
A	Sigma70_r4_2	e2j7aA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
R	1.10.3820.10	Mainly Alpha	Orthogonal Bundle	Multiheme cytochrome fold	Di-heme elbow motif domain	CATH (4.3.0)
O	1.10.3820.10	Mainly Alpha	Orthogonal Bundle	Multiheme cytochrome fold	Di-heme elbow motif domain	CATH (4.3.0)
L	1.10.3820.10	Mainly Alpha	Orthogonal Bundle	Multiheme cytochrome fold	Di-heme elbow motif domain	CATH (4.3.0)
I	1.10.3820.10	Mainly Alpha	Orthogonal Bundle	Multiheme cytochrome fold	Di-heme elbow motif domain	CATH (4.3.0)
F	1.10.3820.10	Mainly Alpha	Orthogonal Bundle	Multiheme cytochrome fold	Di-heme elbow motif domain	CATH (4.3.0)
C	1.10.3820.10	Mainly Alpha	Orthogonal Bundle	Multiheme cytochrome fold	Di-heme elbow motif domain	CATH (4.3.0)
N	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
N	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
Q	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
Q	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
P	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
P	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
M	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
M	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
K	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
K	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
J	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
J	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
H	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
H	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
G	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
G	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
E	1.10.1130.10	Mainly Alpha	Orthogonal Bundle	Flavocytochrome C3	Chain A, domain 2	CATH (4.3.0)
E	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
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)
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, D, E, G A, B, D, E, G, H, J, K, M, N, P, Q	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
C, F, I, L, O C, F, I, L, O, R	CYTOCHROME C QUINOL DEHYDROGENASE NRFH	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	nitrogen cycle metabolic process denitrification pathway metabolic process cellular process cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy anaerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane
A, B, D, E, G A, B, D, E, G, H, J, K, M, N, P, Q	CYTOCHROME C NITRITE REDUCTASE NRFA	oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor oxidoreductase activity nitrite reductase (cytochrome, ammonia-forming) activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitrite reductase activity catalytic activity binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule binding	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane extracellular region outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L, O C, F, I, L, O, R	IPR005126	NapC/NirT cytochrome c, N-terminal	Domain
C, F, I, L, O C, F, I, L, O, R	IPR036280	Multiheme cytochrome superfamily	Homologous Superfamily
C, F, I, L, O C, F, I, L, O, R	IPR024717	Denitrification system component NapC/NirT/NrfH	Family
C, F, I, L, O C, F, I, L, O, R	IPR051174	Cytochrome c-type Electron Transfer	Family
C, F, I, L, O C, F, I, L, O, R	IPR038266	NapC/NirT cytochrome c superfamily	Homologous Superfamily
A, B, D, E, G A, B, D, E, G, H, J, K, M, N, P, Q	IPR036280	Multiheme cytochrome superfamily	Homologous Superfamily
A, B, D, E, G A, B, D, E, G, H, J, K, M, N, P, Q	IPR003321	Cytochrome c552	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	OPM	Transmembrane	Bitopic proteins	Multi-heme cytochromes	Cytochrome c of nitrite reductase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Oxidoreductases	NrfH Cytochrome C Quinol Dehydrogenase