Annotations: 7CZY

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092661	3002615	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092661	3002615	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092661	3002615	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
E [auth K]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	SCOP2B (2022-06-29)
G [auth N]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	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)
A	Spike_NTD	e7czyA2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Spike_NTD	ECOD (1.6)
A	Spike_rec_bind_1	e7czyA3	A: beta complex topology	X: Beta domain of coronavirus spike glycoprotein (From Topology)	H: Beta domain of coronavirus spike glycoprotein (From Topology)	T: Beta domain of coronavirus spike glycoprotein	F: Spike_rec_bind_1	ECOD (1.6)
A	Spike_rec_bind	e7czyA4	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Beta-coronavirus spike protein receptor-binding domain	F: Spike_rec_bind	ECOD (1.6)
A	Corona_S2	e7czyA1	A: a+b complex topology	X: S2 subunit of coronavirus spike glycoprotein (From Topology)	H: S2 subunit of coronavirus spike glycoprotein (From Topology)	T: S2 subunit of coronavirus spike glycoprotein	F: Corona_S2	ECOD (1.6)
B	Spike_NTD	e7czyB4	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Spike_NTD	ECOD (1.6)
B	Spike_rec_bind_1	e7czyB3	A: beta complex topology	X: Beta domain of coronavirus spike glycoprotein (From Topology)	H: Beta domain of coronavirus spike glycoprotein (From Topology)	T: Beta domain of coronavirus spike glycoprotein	F: Spike_rec_bind_1	ECOD (1.6)
B	Spike_rec_bind	e7czyB1	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Beta-coronavirus spike protein receptor-binding domain	F: Spike_rec_bind	ECOD (1.6)
B	Corona_S2	e7czyB2	A: a+b complex topology	X: S2 subunit of coronavirus spike glycoprotein (From Topology)	H: S2 subunit of coronavirus spike glycoprotein (From Topology)	T: S2 subunit of coronavirus spike glycoprotein	F: Corona_S2	ECOD (1.6)
C	Spike_NTD	e7czyC3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Spike_NTD	ECOD (1.6)
C	Spike_rec_bind_1	e7czyC4	A: beta complex topology	X: Beta domain of coronavirus spike glycoprotein (From Topology)	H: Beta domain of coronavirus spike glycoprotein (From Topology)	T: Beta domain of coronavirus spike glycoprotein	F: Spike_rec_bind_1	ECOD (1.6)
C	Spike_rec_bind	e7czyC2	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Beta-coronavirus spike protein receptor-binding domain	F: Spike_rec_bind	ECOD (1.6)
C	Corona_S2	e7czyC1	A: a+b complex topology	X: S2 subunit of coronavirus spike glycoprotein (From Topology)	H: S2 subunit of coronavirus spike glycoprotein (From Topology)	T: S2 subunit of coronavirus spike glycoprotein	F: Corona_S2	ECOD (1.6)
D [auth H]	V-set_8	e7czyH2	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)
D [auth H]	C1-set_1	e7czyH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F [auth J]	V-set_8	e7czyJ2	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)
F [auth J]	C1-set_1	e7czyJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth K]	C1-set_4	e7czyK2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E [auth K]	V-set	e7czyK1	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)
G [auth N]	C1-set_4	e7czyN2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
G [auth N]	V-set	e7czyN1	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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth H], F [auth J]	Heavy Chain	IGHV1	-	spike glycoprotein	SAbDab (2024-12-20)
E [auth K], G [auth N]	Light Chain	IGKV4	Kappa	spike glycoprotein	SAbDab (2024-12-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01601	Coronavirus spike glycoprotein S2 (CoV_S2)	Coronavirus spike glycoprotein S2	-	Family
A, B, C	PF16451	Betacoronavirus-like spike glycoprotein S1, N-terminal (bCoV_S1_N)	Betacoronavirus-like spike glycoprotein S1, N-terminal	This 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 ...	This 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 domain (NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Either the S1 NTD or S1 RBD, or occasionally both, are involved in binding to host receptors. S1 NTD is located on the side of the spike trimer and mainly recognises sugar receptors [2]. For many betacoronaviruses (b-CoVs), for example mouse hepatitis virus (MHV), the RBD is located in the NTD. The structure of the MHV S1 NTD showed the same fold as human galectins (galactose-binding lectin), however it does not bind any sugar; instead, it binds to the carcinoembryonic antigen cell-adhesion molecule CEACAM1) through protein-protein interactions [2]. All three CEACAM21a-binding sites in MHV spikes can be fully occupied by CEACAM1a. It has been shown that CEACAM1a binding to the MHV spike weakens the interactions between S1 and S2 and facilitates the proteolysis of the spike protein and dissociation of S1 [2]. The homologous bovine CoV (BCov) S1 NTD also possesses a galectin fold but binds to sialic acid-containing moieties on host cell membranes, as does the NTD of three other group A b-Covs, namely human CoV (HCoV) OC43, avian b-CoV, and infectious bronchitis virus (IBV) [3]. Despite the S1 NTD of human respiratory b-CoV HKU1 being highly homologous to the NTDs of MHV and bovine CoV, it does not bind to either sugar or human carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) and the RBD is found instead in the S1 RBD domain [3].	Domain
A, B, C	PF09408	Betacoronavirus spike glycoprotein S1, receptor binding (bCoV_S1_RBD)	Betacoronavirus spike glycoprotein S1, receptor binding	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 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
A, B, C	PF19209	Coronavirus spike glycoprotein S1, C-terminal (CoV_S1_C)	Coronavirus spike glycoprotein S1, C-terminal	This 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 ...	This 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 epidemic diarrhea virus spike protein [1].	Domain
D [auth H], F [auth J]	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
D [auth H], F [auth J]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
E [auth K], G [auth N]	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
E [auth K], G [auth N]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Spike glycoprotein	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity host cell surface binding host cell surface receptor binding structural constituent of virion structural molecule activity identical protein binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated perturbation of host defense response suppression by virus of host tetherin activity biological process involved in interspecies interaction between organisms modulation by virus of host process virus-mediated perturbation of host defense response biological process involved in interaction with host viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated perturbation of host defense response suppression by virus of host tetherin activity biological process involved in interspecies interaction between organisms modulation by virus of host process virus-mediated perturbation of host defense response biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host process modulation of process of another organism modulation by virus of host cellular process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host viral gene expression viral translation fusion of virus membrane with host plasma membrane import into cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell endocytosis transport of virus regulation of biological process positive regulation of viral life cycle positive regulation of viral process biological regulation positive regulation of biological process modulation by symbiont of entry into host regulation of viral entry into host cell regulation of viral life cycle regulation of viral process positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction response to host defenses response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus entry receptor-mediated virion attachment to host cell	cellular anatomical structure membrane host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm cellular anatomical structure membrane host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region host cell plasma membrane virion component virion membrane viral membrane viral envelope host cell surface
D [auth H], F [auth J]	Immunoglobulin heavy variable 1-8,Immunoglobulin heavy variable 1-8,chain H of P5A-2F11_2B,Epididymis luminal protein 214,Epididymis luminal protein 214	binding antigen binding	response to stimulus immune response immune system process adaptive immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response immune effector process	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
E [auth K], G [auth N]	IG c168_light_IGKV4-1_IGKJ4,Immunoglobulin kappa constant	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 cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling 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 cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response	cellular anatomical structure extracellular region protein-containing complex IgA immunoglobulin complex immunoglobulin complex extracellular space blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle cellular anatomical structure extracellular region protein-containing complex IgA immunoglobulin complex immunoglobulin complex extracellular space blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, B, C	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain
A, B, C	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, B, C	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
A, B, C	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, B, C	IPR042578	Spike glycoprotein, betacoronavirus	Family
A, B, C	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A, B, C	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A, B, C	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, B, C	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A, B, C	IPR002552	Spike glycoprotein S2, coronavirus	Domain
D [auth H], F [auth J]	IPR003597	Immunoglobulin C1-set	Domain
D [auth H], F [auth J]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth H], F [auth J]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth H], F [auth J]	IPR013106	Immunoglobulin V-set domain	Domain
D [auth H], F [auth J]	IPR003599	Immunoglobulin domain subtype	Domain
D [auth H], F [auth J]	IPR007110	Immunoglobulin-like domain	Domain
D [auth H], F [auth J]	IPR050380	Immune Recognition and Response Modulators	Family
D [auth H], F [auth J]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D [auth H], F [auth J]	IPR050199	Immunoglobulin Heavy Variable	Family
D [auth H], F [auth J]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth H], F [auth J]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth H], F [auth J]	IPR013106	Immunoglobulin V-set domain	Domain
D [auth H], F [auth J]	IPR007110	Immunoglobulin-like domain	Domain
E [auth K], G [auth N]	IPR050150	Immunoglobulin Variable Light Chain	Family
E [auth K], G [auth N]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth K], G [auth N]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth K], G [auth N]	IPR013106	Immunoglobulin V-set domain	Domain
E [auth K], G [auth N]	IPR003599	Immunoglobulin domain subtype	Domain
E [auth K], G [auth N]	IPR007110	Immunoglobulin-like domain	Domain
E [auth K], G [auth N]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth K], G [auth N]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
E [auth K], G [auth N]	IPR003597	Immunoglobulin C1-set	Domain
E [auth K], G [auth N]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth K], G [auth N]	IPR007110	Immunoglobulin-like domain	Domain
E [auth K], G [auth N]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth K], G [auth N]	Pharos: P01834	recurrent infections associated with rare immunoglobulin isotypes deficiency myositis dysgammaglobulinemia Hepatomegaly acquired idiopathic inflammatory myopathy selective IgG immunodeficiency

7CZY

S protein of SARS-CoV-2 in complex bound with P5A-2F11_2B

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

SAbDab Antibody Annotation SAbDab Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation

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7CZY

S protein of SARS-CoV-2 in complex bound with P5A-2F11_2B

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

SAbDab Antibody Annotation SAbDab Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation