5C6T | pdb_00005c6t

Crystal structure of HCMV glycoprotein B in complex with 1G2 Fab

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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	SCOP2 Family	Glycoprotein B-like	8072741	4002622	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Viral glycoprotein ectodomain-like	8072742	3001498	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Glycoprot_B_PH1	e5c6tA2	A: beta barrels	X: PH domain-like	H: first barrel domain in viral glycoproteins (From Topology)	T: first barrel domain in viral glycoproteins	F: Glycoprot_B_PH1	ECOD (1.6)
A	Glycoprot_B_PH2	e5c6tA3	A: beta barrels	X: PH domain-like	H: second barrel domain in viral glycoproteins (From Topology)	T: second barrel domain in viral glycoproteins	F: Glycoprot_B_PH2	ECOD (1.6)
A	Glycoprotein_B	e5c6tA1	A: beta complex topology	X: Viral glycoprotein ectodomain-like (From Topology)	H: Viral glycoprotein ectodomain-like (From Topology)	T: Viral glycoprotein ectodomain-like	F: Glycoprotein_B	ECOD (1.6)
B [auth H]	V-set_8	e5c6tH1	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)
C [auth L]	V-set_3	e5c6tL1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.29.100	Mainly Beta	Roll	PH-domain like		CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

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]	1G2 Fab	VH-CH1	Homo sapiens (human)	IGHV4-3901, IGHV4-3907, IGHJ401, IGHJ402, IGHJ403, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202510-0)
C [auth L]	1G2 Fab	L-LAMBDA	Homo sapiens (human)	IGLV1-4701, IGLJ302, IGLC201, IGLC202, IGLC3*04	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202510-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV4	-	envelope glycoprotein b	SAbDab (2025-03-21)
C [auth L]	Light Chain	IGLV1	Lambda	envelope glycoprotein b	SAbDab (2025-03-21)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00606	Herpesvirus Glycoprotein B ectodomain (Glycoprotein_B)	Herpesvirus Glycoprotein B ectodomain	This domain corresponds to the ectodomain of glycoprotein B according to ECOD.	Domain
A	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	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
A	Envelope 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 host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane 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
B [auth H]	1G2 Fab heavy chain	-	-	-
C [auth L]	1G2 Fab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR035381	Herpesvirus Glycoprotein B, PH-like domain 2	Domain
A	IPR035377	Herpesvirus Glycoprotein B, PH-like domain 1	Domain
A	IPR021044	Herpesvirus Glycoprotein B, antigenic domain, N-terminal	Domain
A	IPR000234	Herpesvirus Glycoprotein B	Family
A	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.