6WAR | pdb_00006war

Crystal structure of the MERS-CoV RBD bound by the neutralizing single-domain antibody MERS VHH-55

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
O	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	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)
P	V-set_1	e6warP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
N	V-set_1	e6warN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
L	V-set_1	e6warL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
J	V-set_1	e6warJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
H	V-set_1	e6warH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
F	V-set_1	e6warF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
D	V-set_1	e6warD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
B	V-set_1	e6warB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
O	Spike_rec_bind	e6warO1	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)
M	Spike_rec_bind	e6warM1	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)
K	Spike_rec_bind	e6warK1	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)
I	Spike_rec_bind	e6warI1	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)
G	Spike_rec_bind	e6warG1	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)
E	Spike_rec_bind	e6warE1	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	Spike_rec_bind	e6warC1	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	Spike_rec_bind	e6warA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
O	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (utative)
O	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (utative)
M	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (utative)
M	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (utative)
K	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (utative)
K	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (utative)
I	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (utative)
I	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (utative)
G	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (utative)
G	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (utative)
E	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (utative)
E	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (utative)
C	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (utative)
C	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (utative)
A	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (utative)
A	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D, F, H, J B, D, F, H, J, L, N, P	Heavy Chain	IGHV1	-	spike protein	SAbDab (2025-10-31)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K, M, O	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, D, F, H, J B, D, F, H, J, L, N, P	nanobody MERS VHH-55	-	-	-
A, C, E, G, I A, C, E, G, I, K, M, O	Spike protein	-	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 membrane organization cellular component organization membrane fusion viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis 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 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	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part 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 virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part 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 viral membrane viral envelope host cell plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044376	Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR042578	Spike glycoprotein, betacoronavirus	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044337	Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	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.