9LH2 | pdb_00009lh2

Crystal structure of SARS-CoV-2 spike receptor-binding domain (Delta) in complex with pH-dependent nanobody MNb-11.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, C [auth D]	Heavy Chain	IGHV3	-	spike protein s1	SAbDab (2026-03-06)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth 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 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
B, C [auth D]	MNb-11	-	-	-
A, D [auth C]	Spike protein S1	molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity host cell surface binding binding host cell surface receptor binding structural constituent of virion structural molecule activity 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 symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host tissue disruption of anatomical structure in another organism symbiont entry into host cell symbiont entry into 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 disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host tissue disruption of anatomical structure in another organism symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host fusion of virus membrane with host plasma membrane 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 entry receptor-mediated virion attachment to host cell	cellular anatomical structure membrane host extracellular space host cellular component other organism part 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 cellular anatomical structure membrane host extracellular space host cellular component other organism part 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth C]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, D [auth C]	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain
A, D [auth C]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, D [auth C]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
A, D [auth C]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, D [auth C]	IPR042578	Spike glycoprotein, betacoronavirus	Family
A, D [auth C]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A, D [auth C]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A, D [auth C]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, D [auth C]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, D [auth C]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A, D [auth C]	IPR002552	Spike glycoprotein S2, coronavirus	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.