3WFB | pdb_00003wfb

Reduced cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth L]	d3wfbl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d3wfbl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d3wfbh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth L]	e3wfbL1	A: HTH	X: Toll/Interleukin receptor TIR domain	H: Toll/Interleukin receptor TIR domain	T: PemK_toxin	F:	ECOD (20:10:01)
C [auth B]	e3wfbB1	A: HTH	X: Toll/Interleukin receptor TIR domain	H: Toll/Interleukin receptor TIR domain	T: PemK_toxin	F:	ECOD (20:10:01)
D [auth C]	e3wfbC1	A: Outer membrane meander beta-barrels	X: Porins	H: Porin	T: Hemagglutinin	F:	ECOD (20:10:01)
B [auth H]	e3wfbH1	A: HTH	X: Toll/Interleukin receptor TIR domain	H: Toll/Interleukin receptor TIR domain	T: PemK_toxin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth B]	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
D [auth C]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth L]	Antibody Fab Fragment	L-KAPPA	Mus musculus (house mouse)	IGKV16-10401, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202609-0)
B [auth H]	Antibody Fab Fragment	VH-CH1	Mus musculus (house mouse)	IGHV1-501, IGHJ101, IGHJ102, IGHJ103, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV16	Kappa	nitric oxide reductase subunit b \| nitric oxide reductase subunit c	SAbDab (2026-03-13)
B [auth H]	Heavy Chain	IGHV1	-	nitric oxide reductase subunit b \| nitric oxide reductase subunit c	SAbDab (2026-03-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B]	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family
D [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L]	antibody fab fragment light chain	-	-	-
C [auth B]	Nitric oxide reductase subunit B	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 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 oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity 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 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 oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding tetrapyrrole binding heme binding 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 respiratory electron transport chain electron transport chain generation of precursor metabolites and energy aerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane
D [auth C]	Nitric oxide reductase subunit C	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 [auth H]	antibody fab fragment heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B]	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
C [auth B]	IPR000883	Cytochrome c oxidase subunit I	Family
C [auth B]	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
C [auth B]	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
D [auth C]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
D [auth C]	IPR009056	Cytochrome c-like domain	Domain
D [auth C]	IPR051811	Cytochrome c550/c551-like	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
C [auth B], D [auth C]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
C [auth B], D [auth C]	MemProtMD	Annotated as membrane protein by MemProtMD

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.

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