8BBO

SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth R]PF09408e8bboR1 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)
B [auth H]PF07654e8bboH2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
B [auth H]PF07686e8bboH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
C [auth L]PF07654e8bboL2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
C [auth L]PF07686e8bboL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
B [auth H]Heavy ChainIGHV4 -spike glycoproteinSAbDab (2024-06-14)
C [auth L]Light ChainIGKV1 Kappaspike glycoproteinSAbDab (2024-06-14)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth R]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
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 L]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
C [auth L]PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth R]Spike glycoprotein-
B [auth H]IGH@ protein
C [auth L]Immunoglobulin kappa light chain-

InterPro: Protein Family Classification InterPro Database Homepage

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