8HC2

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 1 YB9-258 Fab (1 RBD up)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth B]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like 8092467 3001706 SCOP2B (2022-06-29)
A [auth B]SCOP2B SuperfamilyCoronavirus S2 glycoprotein stalk-like 8092471 3000282 SCOP2B (2022-06-29)
A [auth B]SCOP2B SuperfamilyCoronavirus S1 glycoprotein, domain C-like 8092661 3002615 SCOP2B (2022-06-29)
A [auth B]SCOP2B SuperfamilyCoronavirus spike S2 glycoprotein connector domain-like 8092473 3002562 SCOP2B (2022-06-29)
A [auth B]SCOP2B SuperfamilyConcanavalin A-like lectins/glucanases 8092469 3000120 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyCoronavirus S2 glycoprotein stalk-like 8092471 3000282 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyConcanavalin A-like lectins/glucanases 8092469 3000120 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like 8092467 3001706 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyCoronavirus spike S2 glycoprotein connector domain-like 8092473 3002562 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyCoronavirus S1 glycoprotein, domain C-like 8092661 3002615 SCOP2B (2022-06-29)
E [auth A]SCOP2B SuperfamilyCoronavirus S2 glycoprotein stalk-like 8092471 3000282 SCOP2B (2022-06-29)
E [auth A]SCOP2B SuperfamilyConcanavalin A-like lectins/glucanases 8092469 3000120 SCOP2B (2022-06-29)
E [auth A]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like 8092467 3001706 SCOP2B (2022-06-29)
E [auth A]SCOP2B SuperfamilyCoronavirus S1 glycoprotein, domain C-like 8092661 3002615 SCOP2B (2022-06-29)
E [auth A]SCOP2B SuperfamilyCoronavirus spike S2 glycoprotein connector domain-like 8092473 3002562 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth B]Spike_NTDe8hc2B3 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: Spike_NTDECOD (1.6)
A [auth B]Spike_rec_bind_1e8hc2B2 A: beta complex topologyX: Beta domain of coronavirus spike glycoprotein (From Topology)H: Beta domain of coronavirus spike glycoprotein (From Topology)T: Beta domain of coronavirus spike glycoproteinF: Spike_rec_bind_1ECOD (1.6)
A [auth B]Spike_rec_binde8hc2B1 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: Spike_rec_bindECOD (1.6)
A [auth B]Corona_S2e8hc2B4 A: a+b complex topologyX: S2 subunit of coronavirus spike glycoprotein (From Topology)H: S2 subunit of coronavirus spike glycoprotein (From Topology)T: S2 subunit of coronavirus spike glycoproteinF: Corona_S2ECOD (1.6)
B [auth C]Spike_NTDe8hc2C2 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: Spike_NTDECOD (1.6)
B [auth C]Spike_rec_bind_1e8hc2C3 A: beta complex topologyX: Beta domain of coronavirus spike glycoprotein (From Topology)H: Beta domain of coronavirus spike glycoprotein (From Topology)T: Beta domain of coronavirus spike glycoproteinF: Spike_rec_bind_1ECOD (1.6)
B [auth C]Spike_rec_binde8hc2C4 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: Spike_rec_bindECOD (1.6)
B [auth C]Corona_S2e8hc2C1 A: a+b complex topologyX: S2 subunit of coronavirus spike glycoprotein (From Topology)H: S2 subunit of coronavirus spike glycoprotein (From Topology)T: S2 subunit of coronavirus spike glycoproteinF: Corona_S2ECOD (1.6)
E [auth A]Spike_NTDe8hc2A4 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: Spike_NTDECOD (1.6)
E [auth A]Spike_rec_bind_1e8hc2A1 A: beta complex topologyX: Beta domain of coronavirus spike glycoprotein (From Topology)H: Beta domain of coronavirus spike glycoprotein (From Topology)T: Beta domain of coronavirus spike glycoproteinF: Spike_rec_bind_1ECOD (1.6)
E [auth A]Spike_rec_binde8hc2A2 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: Spike_rec_bindECOD (1.6)
E [auth A]Corona_S2e8hc2A3 A: a+b complex topologyX: S2 subunit of coronavirus spike glycoprotein (From Topology)H: S2 subunit of coronavirus spike glycoprotein (From Topology)T: S2 subunit of coronavirus spike glycoproteinF: Corona_S2ECOD (1.6)
C [auth L]C1-set_4e8hc2L1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_4ECOD (1.6)
C [auth L]V-sete8hc2L2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
D [auth H]V-set_8e8hc2H2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
D [auth H]C1-set_1e8hc2H1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
C [auth L]Light ChainIGKV1 Kappaspike glycoproteinSAbDab (2024-12-27)
D [auth H]Heavy ChainIGHV3 -spike glycoproteinSAbDab (2024-12-27)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth B],
B [auth C],
E [auth A]
PF01601Coronavirus spike glycoprotein S2 (CoV_S2)Coronavirus spike glycoprotein S2- Family
A [auth B],
B [auth C],
E [auth A]
PF16451Betacoronavirus-like spike glycoprotein S1, N-terminal (bCoV_S1_N)Betacoronavirus-like spike glycoprotein S1, N-terminalThis entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like doma ...Domain
A [auth B],
B [auth C],
E [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 ...Domain
A [auth B],
B [auth C],
E [auth A]
PF19209Coronavirus spike glycoprotein S1, C-terminal (CoV_S1_C)Coronavirus spike glycoprotein S1, C-terminalThis entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epide ...Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth B],
B [auth C],
E [auth A]
Spike glycoprotein
C [auth L]Light chain of YB9-258 Fab---
D [auth H]Heavy chain of YB9-258 Fab---