8EDF

Bovine Fab SKD in complex with Sars COV-2 receptor binding domain

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
C [auth A]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like8092467 3001706 SCOP2B (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth L]PF07654e8edfL2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
B [auth H]PF07654e8edfH2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
B [auth H]PF07686e8edfH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
C [auth A]PF09408e8edfA1 A: a+b three layersX: Coronavirus spike protein receptor-binding domain (From Homology)H: Coronavirus spike protein receptor-binding domainT: Beta-coronavirus spike protein receptor-binding domainF: PF09408ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
A [auth L]Light ChainIGLV1 Lambdaspike protein s1SAbDab (2024-06-21)
B [auth H]Heavy ChainIGHV1 -spike protein s1SAbDab (2024-06-21)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth L]PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
B [auth H]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
B [auth H]PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
C [auth A]PF09408Betacoronavirus spike glycoprotein S1, receptor binding (bCoV_S1_RBD)Betacoronavirus spike glycoprotein S1, receptor bindingThis entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is transla ...This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion [1]. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilise both the S1 NTD and S1 RBD for viral entry [2]. SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor [3,4].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth L]SKD Fab Light chain
B [auth H]SKD Fab heavy chain
C [auth A]Spike protein S1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth L]IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
A [auth L]IPR003597Immunoglobulin C1-setDomain
A [auth L]IPR013783Immunoglobulin-like foldHomologous Superfamily
A [auth L]IPR007110Immunoglobulin-like domainDomain
A [auth L]IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
B [auth H]IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
B [auth H]IPR003599Immunoglobulin subtypeDomain
B [auth H]IPR003597Immunoglobulin C1-setDomain
B [auth H]IPR013783Immunoglobulin-like foldHomologous Superfamily
B [auth H]IPR013106Immunoglobulin V-set domainDomain
B [auth H]IPR007110Immunoglobulin-like domainDomain
B [auth H]IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
C [auth A]IPR044873Spike glycoprotein S2, coronavirus, heptad repeat 1Domain
C [auth A]IPR044366Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2Domain
C [auth A]IPR018548Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirusDomain
C [auth A]IPR044341Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-likeDomain
C [auth A]IPR032500Spike glycoprotein S1, N-terminal domain, betacoronavirus-likeDomain
C [auth A]IPR042578Spike glycoprotein, betacoronavirusFamily
C [auth A]IPR036326Spike S1 subunit, receptor binding domain superfamily, betacoronavirusHomologous Superfamily
C [auth A]IPR043002Spike glycoprotein, N-terminal domain superfamilyHomologous Superfamily
C [auth A]IPR044874Spike glycoprotein S2, coronavirus, heptad repeat 2Domain
C [auth A]IPR043473Spike glycoprotein S2 superfamily, coronavirusHomologous Superfamily
C [auth A]IPR043607Coronavirus spike glycoprotein S1, C-terminalDomain
C [auth A]IPR002552Spike glycoprotein S2, coronavirusDomain