6ZDG | pdb_00006zdg

Association of three complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth E]	Spike_rec_bind	e6zdgE1	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 A]	Spike_rec_bind	e6zdgA1	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 [auth D]	Spike_rec_bind	e6zdgD1	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 [auth H]	V-set_8	e6zdgH2	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)
B [auth H]	C1-set_1	e6zdgH1	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 B]	V-set_8	e6zdgB1	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)
E [auth B]	C1-set_1	e6zdgB2	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)
H [auth F]	V-set_8	e6zdgF2	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)
H [auth F]	C1-set_1	e6zdgF1	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)
C [auth L]	C1-set_4	e6zdgL2	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)
C [auth L]	V-set	e6zdgL1	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)
F [auth C]	C1-set_4	e6zdgC1	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)
F [auth C]	V-set	e6zdgC2	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)
I [auth G]	C1-set_4	e6zdgG2	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)
I [auth G]	V-set	e6zdgG1	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)

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
B [auth H], E [auth B], H [auth F]	Fab EY6A, anti-SARS-CoV-2 S RBD, neutralizing	VH-CH1	Homo sapiens (human)	IGHV3-3018, IGHV3-30-501, IGHJ401, IGHJ402, IGHJ403, IGHG103, IGHG108, IGHG106	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202525-0)
C [auth L], F [auth C], I [auth G]	Fab EY6A, anti-SARS-CoV-2 S RBD, neutralizing	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ401, IGKJ402, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202525-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H], E [auth B], H [auth F]	Heavy Chain	IGHV3	-	spike glycoprotein	SAbDab (2025-07-04)
C [auth L], F [auth C], I [auth G]	Light Chain	IGKV1	Kappa	spike glycoprotein	SAbDab (2025-07-04)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], D [auth A], G [auth D]	Spike protein S1	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 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 viral gene expression viral translation 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 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
B [auth H], E [auth B], H [auth F]	EY6A heavy chain	-	-	-
C [auth L], F [auth C], I [auth G]	EY6A light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], D [auth A], G [auth D]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A [auth E], D [auth A], G [auth D]	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain
A [auth E], D [auth A], G [auth D]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A [auth E], D [auth A], G [auth D]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
A [auth E], D [auth A], G [auth D]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A [auth E], D [auth A], G [auth D]	IPR042578	Spike glycoprotein, betacoronavirus	Family
A [auth E], D [auth A], G [auth D]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A [auth E], D [auth A], G [auth D]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A [auth E], D [auth A], G [auth D]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A [auth E], D [auth A], G [auth D]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A [auth E], D [auth A], G [auth D]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A [auth E], D [auth A], G [auth D]	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.