6NB4 | pdb_00006nb4

MERS-CoV S complex with human neutralizing LCA60 antibody Fab fragment (state 2)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody 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)
C	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092681	3002615	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092538	3002562	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092534	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092536	3000282	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092536	3000282	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092534	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092538	3002562	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092681	3002615	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092538	3002562	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092532	3001706	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092536	3000282	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092681	3002615	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092534	3000120	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)
E [auth L]	V-set_3	e6nb4L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D [auth H]	V-set_12	e6nb4H1	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	Spike_NTD	e6nb4C2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Spike_NTD	ECOD (1.6)
C	Corona_S1_3rd	e6nb4C3	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: Corona_S1_3rd	ECOD (1.6)
C	Corona_S2	e6nb4C1	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	e6nb4B2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Spike_NTD	ECOD (1.6)
B	Corona_S1_3rd	e6nb4B3	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: Corona_S1_3rd	ECOD (1.6)
B	Corona_S2	e6nb4B1	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)
A	Spike_NTD	e6nb4A1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Spike_NTD	ECOD (1.6)
A	Corona_S1_3rd	e6nb4A5	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: Corona_S1_3rd	ECOD (1.6)
A	Spike_rec_bind	e6nb4A3	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	e6nb4A4	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)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
E [auth L]	LCA60 Fv, anti- MERS-CoV RBD, neutralizing	V-LAMBDA	Homo sapiens (human)	IGLV2-2301, IGLV2-2302, IGLV2-2303, IGLJ201, IGLJ3*01	V-DOMAIN V-LAMBDA	IG	FV-HEAVY_LAMBDA	IMGT (202602-0)
D [auth H]	LCA60 Fv, anti- MERS-CoV RBD, neutralizing	VH	Homo sapiens (human)	IGHV3-1501, IGHV3-1505, IGHJ401, IGHJ402, IGHJ4*03	V-DOMAIN VH	IG	FV-HEAVY_LAMBDA	IMGT (202602-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth L]	Light Chain	IGLV2	Lambda	spike glycoprotein	SAbDab (2026-01-23)
D [auth H]	Heavy Chain	IGHV3	-	spike glycoprotein	SAbDab (2026-01-23)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth L]	LCA60 light chain	-	-	-
D [auth H]	LCA60 heavy chain	-	-	-
A, B, C	Spike glycoprotein	-	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 fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell	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, B, C	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, B, C	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, B, C	IPR044376	Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV	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	IPR044337	Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like	Domain
A, B, C	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
A, B, C	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	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

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.