2gum

Crystal structure of the extracellular domain of glycoprotein B from Herpes Simplex Virus type I

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycoprotein B

Human herpesvirus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SODIUM ION × 4 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGLB_HHV1K
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–628； UniProt 103–730 Author chain B； PDBConstruct 1–628； UniProt 103–730 Author chain C； PDBConstruct 1–628； UniProt 103–730

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2gum
Deposition date deposition_date	2006-05-01
Structure title title	Crystal structure of the extracellular domain of glycoprotein B from Herpes Simplex Virus type I
Keywords keywords	ENVELOPE GLYCOPROTEIN, MEMBRANE FUSION, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2gum__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2gum__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gum__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	50.56 Å
Rg (electron density)	50.93 Å
Total Rg	50.86 Å
Atom count	14000
Residues	1732
Excluded volume	246500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gum__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Glycoprotein B
Molecular weight formula_weight	71668.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	14223

DIKAENTDANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTTYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYQANGGFLIAYQPLLSNTLAELYVREHLREQSRKPPNPTPPPPGASANASVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIHADANAA

Source Source

Source organism organism	Human herpesvirus 1
NCBI taxonomy ID ncbi_taxonomy_id	10306
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2guma1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamily	e.76.1 — Viral glycoprotein ectodomain-like
Family Family family	e.76.1.1 — Glycoprotein B-like

Domain ID domain_id	d2gumb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamily	e.76.1 — Viral glycoprotein ectodomain-like
Family Family family	e.76.1.1 — Glycoprotein B-like

Domain ID domain_id	d2gumc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamily	e.76.1 — Viral glycoprotein ectodomain-like
Family Family family	e.76.1.1 — Glycoprotein B-like

CATH v4.4 (12 domains)

Domain ID domain_id	2gumA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1230 —

Domain ID domain_id	2gumA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1890 —

Domain ID domain_id	2gumA03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	2gumA05
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3280 —

Domain ID domain_id	2gumB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1230 —

Domain ID domain_id	2gumB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1890 —

Domain ID domain_id	2gumB03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	2gumB05
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3280 —

Domain ID domain_id	2gumC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1230 —

Domain ID domain_id	2gumC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1890 —

Domain ID domain_id	2gumC03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	2gumC05
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3280 —

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Unit-cell length a length_a	84.959 Å
Unit-cell length b length_b	100.039 Å
Unit-cell length c length_c	100.133 Å
Unit-cell angle α angle_alpha	67.04 °
Unit-cell angle β angle_beta	77.99 °
Unit-cell angle γ angle_gamma	70.31 °
Molecules per unit cell Z z_pdb	3

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	41.200 Å
R factor r_factor	0.2479
R_work r_work	0.2479
R_free r_free	0.2747

Crystal structure of the extracellular domain of glycoprotein B from Herpes Simplex Virus type I

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycoprotein B

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2gum__assembly_1__model_1

2gum__assembly_1__model_1 | I(q)

2gum__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (3 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of the extracellular domain of glycoprotein B from Herpes Simplex Virus type I

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycoprotein B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2gum__assembly_1__model_1

2gum__assembly_1__model_1 | I(q)

2gum__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (3 domains)

CATH v4.4 (12 domains)

7. Citations (1)