5VOD | pdb_00005vod

Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G [auth L]	C1-set_4	e5vodL1	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)
G [auth L]	V-set	e5vodL2	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 H]	V-set_8	e5vodH2	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)
F [auth H]	C1-set_1	e5vodH1	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	UNK_F_TYPE	e5vodE1	A: beta barrels	X: UL131A-like	H: UL131A (From Topology)	T: UL131A	F: UNK_F_TYPE	ECOD (1.6)
D	UNK_F_TYPE	e5vodD1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: UNK_F_TYPE	ECOD (1.6)
D	UNK_F_TYPE	e5vodD2	A: beta barrels	X: UL131A-like	H: UL130 C-terminal domain (From Topology)	T: UL130 C-terminal domain	F: UNK_F_TYPE	ECOD (1.6)
C	UNK_F_TYPE	e5vodC1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: UNK_F_TYPE	ECOD (1.6)
C	UNK_F_TYPE	e5vodC2	A: beta barrels	X: UL128 C-terminal domain (From Topology)	H: UL128 C-terminal domain (From Topology)	T: UL128 C-terminal domain	F: UNK_F_TYPE	ECOD (1.6)
B	UNK_F_TYPE	e5vodB2	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: UNK_F_TYPE	ECOD (1.6)
B	UNK_F_TYPE	e5vodB1	A: alpha arrays	X: beta-herpesvirus envelope glycoprotein L (gL) N-terminal domain (From Topology)	H: beta-herpesvirus envelope glycoprotein L (gL) N-terminal domain (From Topology)	T: beta-herpesvirus envelope glycoprotein L (gL) N-terminal domain	F: UNK_F_TYPE	ECOD (1.6)
A	Herpes_glycoH_C	e5vodA1	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	e5vodA2	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)

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
G [auth L]	Fab 9I6, neutralizing	L-KAPPA	Homo sapiens (human)	IGKV2-3001, IGKJ204, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202604-0)
F [auth H]	Fab 9I6, neutralizing	VH-CH1	Homo sapiens (human)	IGHV5-5101, IGHV5-5103, IGHJ302, IGHG103, IGHG108, IGHG106	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202604-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth L]	Light Chain	IGKV2	Kappa	envelope glycoprotein ul128 \| envelope glycoprotein ul131a	SAbDab (2026-02-06)
F [auth H]	Heavy Chain	IGHV5	-	envelope glycoprotein ul128 \| envelope glycoprotein ul131a	SAbDab (2026-02-06)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF11668	HCMV glycoprotein pUL130 (Gp_UL130)	HCMV glycoprotein pUL130	-	Family
A	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	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth L]	Fab 9I6 light chain	cation binding ion binding binding metal ion binding small molecule binding	response to stimulus immune response immune system process adaptive immune response	cellular anatomical structure extracellular region cell periphery plasma membrane membrane protein-containing complex immunoglobulin complex
F [auth H]	Fab 9I6 heavy chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
E	Envelope glycoprotein UL131A	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment 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	virion component viral membrane viral envelope virion membrane
D	Envelope glycoprotein UL130	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment 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	virion component viral membrane viral envelope virion membrane
C	Envelope glycoprotein UL128	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment 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	virion component virion membrane
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 virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral life cycle 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 virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell 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	virion component viral membrane viral envelope host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part virion membrane host intracellular part host cell cytoplasm host cell Golgi apparatus host intracellular region virion component viral membrane viral envelope host cell plasma membrane host cellular component cellular anatomical structure 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
A	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 virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral life cycle 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 virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell 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	cell periphery cellular anatomical structure plasma membrane membrane virion component viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion membrane host intracellular membrane-bounded organelle cell periphery cellular anatomical structure plasma membrane membrane virion component viral membrane viral envelope 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth L]	IPR050150	Immunoglobulin Variable Light Chain	Family
G [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
G [auth L]	IPR003597	Immunoglobulin C1-set	Domain
G [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
G [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
G [auth L]	IPR003599	Immunoglobulin domain subtype	Domain
G [auth L]	IPR007110	Immunoglobulin-like domain	Domain
G [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
F [auth H]	IPR003597	Immunoglobulin C1-set	Domain
F [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
F [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
F [auth H]	IPR013106	Immunoglobulin V-set domain	Domain
F [auth H]	IPR003599	Immunoglobulin domain subtype	Domain
F [auth H]	IPR007110	Immunoglobulin-like domain	Domain
F [auth H]	IPR050380	Immune Recognition and Response Modulators	Family
F [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D	IPR021038	Herpesvirus UL130, cytomegalovirus	Family
C	IPR057762	UL128-like, Cytomegalovirus	Family
B	IPR002689	Cytomegalovirus glycoprotein L	Family
A	IPR038172	Herpesvirus glycoprotein H, C-terminal domain superfamily	Homologous Superfamily
A	IPR003493	Herpesvirus glycoprotein H	Family
A	IPR035305	Herpesvirus glycoprotein H, C-terminal	Domain