6WAQ | pdb_00006waq

Crystal structure of the SARS-CoV-1 RBD bound by the cross-reactive single-domain antibody SARS VHH-72

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6waqa1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
A	d6waqa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d6waqc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d6waqc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
B [auth D]	d6waqd1	Alpha and beta proteins (a+b)	SARS receptor-binding domain-like	SARS receptor-binding domain-like	SARS receptor-binding domain-like	Spike protein S1	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)
B [auth D]	d6waqd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)
D [auth B]	d6waqb1	Alpha and beta proteins (a+b)	SARS receptor-binding domain-like	SARS receptor-binding domain-like	SARS receptor-binding domain-like	Spike protein S1	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)
D [auth B]	d6waqb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth D]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8041894	3001706	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8041894	3001706	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	V-set_12	e6waqA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
C	V-set_12	e6waqC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
B [auth D]	Spike_rec_bind	e6waqD1	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)
D [auth B]	Spike_rec_bind	e6waqB1	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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C	Heavy Chain	IGHV1	-	spike glycoprotein	SAbDab (2025-04-25)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D], D [auth B]	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 translat ...	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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	nanobody SARS VHH-72	-	-	-
B [auth D], D [auth B]	Spike glycoprotein	host cell surface binding binding host cell surface receptor binding identical protein binding 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 virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to 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 virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction fusion of virus membrane with host plasma membrane symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process symbiont-mediated-mediated suppression of host tetherin activity modulation of process of another organism 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 symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component 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 cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D], D [auth B]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
B [auth D], D [auth B]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
B [auth D], D [auth B]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
B [auth D], D [auth B]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
B [auth D], D [auth B]	IPR042578	Spike glycoprotein, betacoronavirus	Family
B [auth D], D [auth B]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
B [auth D], D [auth B]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
B [auth D], D [auth B]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
B [auth D], D [auth B]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
B [auth D], D [auth B]	IPR002552	Spike glycoprotein S2, coronavirus	Domain
B [auth D], D [auth B]	IPR044370	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.