6C5V

An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of vulnerability on Epstein-Barr virus

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Herpes_glycoH_C	e6c5vA2	A: beta sandwiches	X: C-terminal domain of envelope glycoprotein H (From Topology)	H: C-terminal domain of envelope glycoprotein H (From Topology)	T: C-terminal domain of envelope glycoprotein H	F: Herpes_glycoH_C	ECOD (1.6)
A	Herpes_glycop_H	e6c5vA1	A: a+b complex topology	X: gH main domain (From Topology)	H: gH main domain (From Topology)	T: gH main domain	F: Herpes_glycop_H	ECOD (1.6)
B	Phage_glycop_gL	e6c5vB1	A: a+b complex topology	X: gH main domain (From Topology)	H: gH main domain (From Topology)	T: gH main domain	F: Phage_glycop_gL	ECOD (1.6)
C	Lectin_C_2	e6c5vC1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: Lectin_C_2	ECOD (1.6)
D [auth H]	V-set_8	e6c5vH1	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)
D [auth H]	C1-set_1	e6c5vH2	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 L]	C1-set	e6c5vL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
E [auth L]	V-set_3	e6c5vL2	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)

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
D [auth H]	Fab AMMO1, neutralizing antibody	VH-CH1	Homo sapiens (human)	IGHV1-1801, IGHV1-1804, IGHJ401, IGHJ402, IGHJ403, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202450-0)
E [auth L]	Fab AMMO1, neutralizing antibody	L-LAMBDA	Homo sapiens (human)	IGLV3-2101, IGLJ101, IGLC102, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202450-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth H]	Heavy Chain	IGHV1	-	envelope glycoprotein h \| glycoprotein 42 \| envelope glycoprotein l	SAbDab (2024-12-20)
E [auth L]	Light Chain	IGLV3	Lambda	envelope glycoprotein h \| glycoprotein 42 \| envelope glycoprotein l	SAbDab (2024-12-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF11108	Viral glycoprotein L (Phage_glycop_gL)	Viral glycoprotein L	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Envelope glycoprotein H	-	-	-
B	Envelope glycoprotein L	-	membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane viral process cellular process cellular component organization or biogenesis membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms 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 component viral membrane viral envelope cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular part host cell cytoplasm host cell Golgi apparatus host intracellular region virion component viral membrane viral envelope cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular part host cell cytoplasm host cell Golgi apparatus host intracellular region host cell cytoplasm part
C	Glycoprotein 42	binding carbohydrate binding	-	cellular anatomical structure membrane virion component virion membrane
D [auth H]	Antibody Fab AMMO1 heavy chain	-	-	-
E [auth L]	Antibody Fab AMMO1 light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR034708	Envelope glycoprotein L	Family
B	IPR038313	Herpesvirus glycoprotein L, rhadinovirus-type superfamily	Homologous Superfamily
B	IPR020175	Herpesvirus glycoprotein L, rhadinovirus-type	Family
C	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
C	IPR016187	C-type lectin fold	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.