9DD7 | pdb_00009dd7

Cryo-EM structure of neutralizing human antibody D48 in complex with HSV-1 glycoprotein B trimer gB-Ecto.516P.531E.DS

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 [auth E]	SCOP2B Superfamily	Viral glycoprotein ectodomain-like	8098472	3001498	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	Viral glycoprotein ectodomain-like	8098472	3001498	SCOP2B (2022-06-29)
B [auth F]	SCOP2B Superfamily	Viral glycoprotein ectodomain-like	8098472	3001498	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth M], H [auth N], I [auth O]	Light Chain	IGKV1	Kappa	glycoprotein b	SAbDab (2025-11-28)
D [auth I], E [auth J], F [auth K]	Heavy Chain	IGHV3	-	glycoprotein b	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], B [auth F], C [auth G]	PF17417	Herpesvirus Glycoprotein B PH-like domain (Glycoprot_B_PH2)	Herpesvirus Glycoprotein B PH-like domain	This domain corresponds to the second PH-like domain in herpesvirus glycoprotein B.	Domain
A [auth E], B [auth F], C [auth G]	PF17416	Herpesvirus Glycoprotein B (Glycoprot_B_PH1)	Herpesvirus Glycoprotein B	This domain has a PH-like fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth M], H [auth N], I [auth O]	D48 light chain	-	-	-
D [auth I], E [auth J], F [auth K]	D48 heavy chain	-	-	-
A [auth E], B [auth F], C [auth G]	Glycoprotein B	-	virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	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 endosome membrane host cell cytoplasm host cell part 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 endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region viral membrane viral envelope host cell plasma membrane host cell Golgi membrane host cell Golgi apparatus host cell endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], B [auth F], C [auth G]	IPR035381	Herpesvirus Glycoprotein B, PH-like domain 2	Domain
A [auth E], B [auth F], C [auth G]	IPR035377	Herpesvirus Glycoprotein B, PH-like domain 1	Domain
A [auth E], B [auth F], C [auth G]	IPR055341	Herpesvirus glycoprotein B ectodomain C-terminal	Domain
A [auth E], B [auth F], C [auth G]	IPR000234	Herpesvirus Glycoprotein B	Family
A [auth E], B [auth F], C [auth G]	IPR038631	Herpesvirus Glycoprotein B, PH-like domain 2 superfamily	Homologous Superfamily

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.