1AR1 | pdb_00001ar1

Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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
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)
C	d1ar1c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1ar1a_	Membrane and cell surface proteins and peptides	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Bacterial aa3 type cytochrome c oxidase subunit I	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d1ar1b1	All beta proteins	Cupredoxin-like	Cupredoxins	Periplasmic domain of cytochrome c oxidase subunit II	Cytochrome c oxidase	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d1ar1b2	Membrane and cell surface proteins and peptides	Transmembrane helix hairpin	Cytochrome c oxidase subunit II-like, transmembrane region	Cytochrome c oxidase subunit II-like, transmembrane region	Bacterial aa3 type cytochrome c oxidase subunit II	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
D	d1ar1d_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cytochrome c oxidase subunit I-like	8025424	4001989	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytochrome c oxidase subunit I-like	8037803	3000653	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8041053	3000886	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome c oxidase subunit II-like, transmembrane region	8041054	3000692	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	V-set_8	e1ar1C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A	COX1	e1ar1A1	A: alpha superhelices	X: Cytochrome c oxidase subunit I-like	H: Cytochrome c oxidase subunit I-like (From Topology)	T: Cytochrome c oxidase subunit I-like	F: COX1	ECOD (1.6)
B	COX2	e1ar1B1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
B	COX2_TM	e1ar1B2	A: extended segments	X: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	H: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	T: Cytochrome c oxidase subunit II-like, transmembrane region	F: COX2_TM	ECOD (1.6)
D	V-set	e1ar1D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
B	1.10.287.90	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D	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
C	1AR1	VH	Mus musculus (house mouse)	IGHV5-12-201, IGHJ401	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202527-0)
D	1AR1	V-KAPPA	Mus musculus (house mouse)	IGKV12-4401, IGKJ101, IGKJ2*01	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202527-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Heavy Chain	IGHV5	-	cytochrome c oxidase	SAbDab (2025-07-18)
D	Light Chain	IGKV12	Kappa	cytochrome c oxidase	SAbDab (2025-07-18)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family
B	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain		Domain
B	PF02790	Cytochrome C oxidase subunit II, transmembrane domain (COX2_TM)	Cytochrome C oxidase subunit II, transmembrane domain	-	Family
D	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	ANTIBODY FV FRAGMENT	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process	protein-containing complex immunoglobulin complex cellular anatomical structure extracellular region
A	CYTOCHROME C OXIDASE	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 inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding 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 inorganic molecular entity transmembrane transporter activity inorganic cation 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	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	respiratory chain complex protein-containing complex cellular anatomical structure cytochrome complex catalytic complex transmembrane transporter complex membrane membrane protein complex respiratory chain complex IV transporter complex cell periphery plasma membrane
B	CYTOCHROME C OXIDASE	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding 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 cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding 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 inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane
D	ANTIBODY FV FRAGMENT	-	response to stimulus immune response immune system process adaptive immune response	protein-containing complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR050199	Immunoglobulin Heavy Variable	Family
C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C	IPR013106	Immunoglobulin V-set domain	Domain
C	IPR007110	Immunoglobulin-like domain	Domain
A	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A	IPR000883	Cytochrome c oxidase subunit I	Family
A	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
A	IPR033944	Cytochrome c oxidase subunit I domain	Domain
A	IPR014241	Cytochrome c oxidase, subunit I bacterial type	Family
B	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B	IPR011759	Cytochrome C oxidase subunit II, transmembrane domain	Domain
B	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
B	IPR008972	Cupredoxin	Homologous Superfamily
B	IPR001505	Copper centre Cu(A)	Binding Site
B	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
B	IPR014222	Cytochrome c oxidase, subunit II	Domain
D	IPR050150	Immunoglobulin Variable Light Chain	Family
D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D	IPR013106	Immunoglobulin V-set domain	Domain
D	IPR003599	Immunoglobulin domain subtype	Domain
D	IPR007110	Immunoglobulin-like domain	Domain