1AR1 | pdb_00001ar1

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


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilyCytochrome c oxidase subunit I-like 8025424 4001989 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyCytochrome c oxidase subunit I-like 8037803 3000653 SCOP2 (2022-06-29)
BSCOP2B SuperfamilyCupredoxins 8041053 3000886 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCytochrome c oxidase subunit II-like, transmembrane region 8041054 3000692 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
CV-set_8e1ar1C1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
DV-sete1ar1D1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
ACOX1e1ar1A1 A: alpha superhelicesX: Cytochrome c oxidase subunit I-likeH: Cytochrome c oxidase subunit I-like (From Topology)T: Cytochrome c oxidase subunit I-likeF: COX1ECOD (1.6)
BCOX2e1ar1B1 A: beta sandwichesX: Cupredoxin-likeH: Cupredoxin-related (From Topology)T: Cupredoxin-relatedF: COX2ECOD (1.6)
BCOX2_TMe1ar1B2 A: extended segmentsX: 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 regionF: COX2_TMECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
C2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
D2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
A1.20.210.10 Mainly Alpha Up-down Bundle Cytochrome C Oxidase Chain ACATH (4.3.0)
B2.60.40.420 Mainly Beta Sandwich Immunoglobulin-like Cupredoxins - blue copper proteinsCATH (4.3.0)
B1.10.287.90 Mainly Alpha Orthogonal Bundle Helix Hairpins CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
1AR1 VH Mus musculus (house mouse) IGHV5-12-2*01, IGHJ4*01 V-DOMAIN VH IG FV-HEAVY_KAPPA IMGT (202524-0)
1AR1 V-KAPPA Mus musculus (house mouse) IGKV12-44*01, IGKJ1*01, IGKJ2*01 V-DOMAIN V-KAPPA IG FV-HEAVY_KAPPA IMGT (202524-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
Heavy ChainIGHV5 -cytochrome c oxidaseSAbDab (2025-06-27)
Light ChainIGKV12 Kappacytochrome c oxidaseSAbDab (2025-06-27)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. Domain
PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. Domain
PF00115Cytochrome C and Quinol oxidase polypeptide I (COX1)Cytochrome C and Quinol oxidase polypeptide I- Family
PF00116Cytochrome C oxidase subunit II, periplasmic domain (COX2)Cytochrome C oxidase subunit II, periplasmic domainDomain
PF02790Cytochrome C oxidase subunit II, transmembrane domain (COX2_TM)Cytochrome C oxidase subunit II, transmembrane domain- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
ANTIBODY FV FRAGMENT
ANTIBODY FV FRAGMENT-
CYTOCHROME C OXIDASE
CYTOCHROME C OXIDASE

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage