5W0K | pdb_00005w0k

Crystal structure of EBV gHgL/CL40/gp42 N-domain

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)
G [auth D]	SCOP2B Superfamily	Interleukin 8-like chemokines	8091615	3001955	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Interleukin 8-like chemokines	8091615	3001955	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)
F [auth C]	Herpes_glycoH_C	e5w0kC1	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)
F [auth C]	Herpes_glycop_H	e5w0kC2	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)
A	Herpes_glycoH_C	e5w0kA1	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	e5w0kA2	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)
I [auth F]	C1-set_4	e5w0kF2	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 F]	V-set	e5w0kF1	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)
D [auth L]	C1-set_4	e5w0kL2	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)
D [auth L]	V-set	e5w0kL1	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)
H [auth E]	V-set_8	e5w0kE2	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 E]	C1-set_1	e5w0kE1	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 H]	V-set_8	e5w0kH1	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 H]	C1-set_1	e5w0kH2	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)
G [auth D]	Phage_glycop_gL	e5w0kD1	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)
B	Phage_glycop_gL	e5w0kB1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth C]	3.90.380.20	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
A	3.90.380.20	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
I [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth D]	3.10.390.20	Alpha Beta	Roll	SAND domain	Viral glycoprotein L	CATH (4.3.0)
B	3.10.390.20	Alpha Beta	Roll	SAND domain	Viral glycoprotein L	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
D [auth L], I [auth F]	CL40 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV6-1501, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202545-4)
C [auth H], H [auth E]	CL40 Fab	VH-CH1	Mus musculus (house mouse)	IGHV1S12701, IGHJ201, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202545-4)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth L], I [auth F]	Light Chain	IGKV6	Kappa	envelope glycoprotein h	SAbDab (2025-11-14)
C [auth H], H [auth E]	Heavy Chain	IGHV1	-	envelope glycoprotein h	SAbDab (2025-11-14)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F [auth C]	PF17488	Herpesvirus glycoprotein H C-terminal domain (Herpes_glycoH_C)	Herpesvirus glycoprotein H C-terminal domain	Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein [2]. Complex formation between gH and gL has been demonstrated in both virions and infected cells [1]. This entry represents the C-terminal domain.	Domain
A, F [auth C]	PF02489	Herpesvirus glycoprotein H main domain (Herpes_glycop_H)	Herpesvirus glycoprotein H main domain	Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein [2]. Complex formation between gH and gL has been demonstrated in both virions and infected cells [1].	Domain
B, G [auth D]	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, F [auth C]	Envelope glycoprotein H	-	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 other organism part virion membrane host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part virion component viral membrane viral envelope cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion membrane host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell endosome host intracellular region
E [auth X], J [auth Y]	Glycoprotein 42	binding carbohydrate binding	-	host cellular component cellular anatomical structure host cell part host cell membrane other organism part membrane virion component virion membrane
D [auth L], I [auth F]	CL40 IgG light chain	-	-	-
C [auth H], H [auth E]	CL40 IgG heavy chain	-	-	-
B, G [auth D]	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 other organism part virion membrane host intracellular part host cell cytoplasm host cell Golgi apparatus virion component viral membrane viral envelope cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion membrane host intracellular part host cell cytoplasm host cell Golgi apparatus host intracellular region host cell cytoplasm part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F [auth C]	IPR038172	Herpesvirus glycoprotein H, C-terminal domain superfamily	Homologous Superfamily
A, F [auth C]	IPR003493	Herpesvirus glycoprotein H	Family
A, F [auth C]	IPR035305	Herpesvirus glycoprotein H, C-terminal	Domain
E [auth X], J [auth Y]	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
E [auth X], J [auth Y]	IPR016187	C-type lectin fold	Homologous Superfamily
B, G [auth D]	IPR034708	Envelope glycoprotein L	Family
B, G [auth D]	IPR038313	Herpesvirus glycoprotein L, rhadinovirus-type superfamily	Homologous Superfamily
B, G [auth D]	IPR020175	Herpesvirus glycoprotein L, rhadinovirus-type	Family

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.