3NW8 | pdb_00003nw8

Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3nw8d_	Multi-domain proteins (alpha and beta)	Viral glycoprotein ectodomain-like	Viral glycoprotein ectodomain-like	Glycoprotein B-like	Glycoprotein B	HHV-1 (Human alphaherpesvirus 1 strain KOS ) [TaxId: 10306 ],	SCOPe (2.08)
C	d3nw8c_	Multi-domain proteins (alpha and beta)	Viral glycoprotein ectodomain-like	Viral glycoprotein ectodomain-like	Glycoprotein B-like	Glycoprotein B	HHV-1 (Human alphaherpesvirus 1 strain KOS ) [TaxId: 10306 ],	SCOPe (2.08)
B [auth A]	d3nw8a_	Multi-domain proteins (alpha and beta)	Viral glycoprotein ectodomain-like	Viral glycoprotein ectodomain-like	Glycoprotein B-like	Glycoprotein B	HHV-1 (Human alphaherpesvirus 1 strain KOS ) [TaxId: 10306 ],	SCOPe (2.08)
A [auth B]	d3nw8b_	Multi-domain proteins (alpha and beta)	Viral glycoprotein ectodomain-like	Viral glycoprotein ectodomain-like	Glycoprotein B-like	Glycoprotein B	HHV-1 (Human alphaherpesvirus 1 strain KOS ) [TaxId: 10306 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Viral glycoprotein ectodomain-like	8034129	3001498	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Viral glycoprotein ectodomain-like	8034129	3001498	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Viral glycoprotein ectodomain-like	8034129	3001498	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Viral glycoprotein ectodomain-like	8034129	3001498	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)
D	Glycoprot_B_PH1	e3nw8D1	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)
D	Glycoprot_B_PH2	e3nw8D2	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)
D	Glycoprotein_B	e3nw8D3	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)
C	Glycoprot_B_PH1	e3nw8C1	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)
C	Glycoprot_B_PH2	e3nw8C2	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)
C	Glycoprotein_B	e3nw8C3	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 A]	Glycoprot_B_PH1	e3nw8A1	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)
B [auth A]	Glycoprot_B_PH2	e3nw8A2	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)
B [auth A]	Glycoprotein_B	e3nw8A3	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)
A [auth B]	Glycoprot_B_PH1	e3nw8B5	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 [auth B]	Glycoprot_B_PH2	e3nw8B6	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 [auth B]	Glycoprotein_B	e3nw8B4	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.30.1230	Mainly Beta	Roll	SH3 type barrels.		CATH (4.2.0)
D	1.20.5.1890	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)
D	2.30.29.100	Mainly Beta	Roll	PH-domain like		CATH (4.2.0)
D	6.10.250.3280	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)
C	2.30.30.1230	Mainly Beta	Roll	SH3 type barrels.		CATH (4.2.0)
C	1.20.5.1890	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)
C	2.30.29.100	Mainly Beta	Roll	PH-domain like		CATH (4.2.0)
C	6.10.250.3280	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)
B [auth A]	2.30.30.1230	Mainly Beta	Roll	SH3 type barrels.		CATH (4.2.0)
B [auth A]	1.20.5.1890	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)
B [auth A]	2.30.29.100	Mainly Beta	Roll	PH-domain like		CATH (4.2.0)
B [auth A]	6.10.250.3280	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)
A [auth B]	2.30.30.1230	Mainly Beta	Roll	SH3 type barrels.		CATH (4.2.0)
A [auth B]	1.20.5.1890	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)
A [auth B]	2.30.29.100	Mainly Beta	Roll	PH-domain like		CATH (4.2.0)
A [auth B]	6.10.250.3280	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth A], C, D	Envelope glycoprotein B	identical protein binding protein binding binding	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 B], B [auth A], C, D	IPR035381	Herpesvirus Glycoprotein B, PH-like domain 2	Domain
A [auth B], B [auth A], C, D	IPR035377	Herpesvirus Glycoprotein B, PH-like domain 1	Domain
A [auth B], B [auth A], C, D	IPR055341	Herpesvirus glycoprotein B ectodomain C-terminal	Domain
A [auth B], B [auth A], C, D	IPR000234	Herpesvirus Glycoprotein B	Family
A [auth B], B [auth A], C, D	IPR038631	Herpesvirus Glycoprotein B, PH-like domain 2 superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth B], B [auth A], C, D	OPM	Transmembrane	Bitopic proteins	Viral membrane fusion glycoprotein	Herpesvirus glycoprotein B

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.