SAXSdb — 1l2g

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

Glycoprotein D

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 2	2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 8	2-acetamido-2-deoxy-beta-D-glucopyranose × 8	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 8	2-acetamido-2-deoxy-beta-D-glucopyranose × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGLD_HHV1P
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–287； UniProt 26–310 Author chain B； PDBConstruct 3–287； UniProt 26–310 Author chain C； PDBConstruct 3–287； UniProt 26–310 Author chain D； PDBConstruct 3–287； UniProt 26–310

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	1l2g
Deposition date deposition_date	2002-02-21
Structure title title	Structure of a C-terminally truncated form of glycoprotein D from HSV-1
Keywords keywords	Ig fold, viral envelope glycoprotein, 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.

1l2g__assembly_4__model_2

Assembly 4 · Model 2 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1l2g__assembly_4__model_2 | I(q)

100 plotted points; both axes use logarithmic scales.

1l2g__assembly_4__model_2 | P(r) · Pending

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

Rg（Guinier）	41.93 Å
Rg (electron density)	40.92 Å
Total Rg	41.37 Å
Atom count	15376
Residues	1936
Excluded volume	274930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1l2g__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`1l2g__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1l2g__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	2	`1l2g__assembly_2__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1l2g__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	2	`1l2g__assembly_3__model_2`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1l2g__assembly_4__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	2	`1l2g__assembly_4__model_2`	octameric （8）	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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1l2ga_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1l2gb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1l2gc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1l2gd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	1l2gA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	230 — Glycoprotein D; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2gB00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	230 — Glycoprotein D; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2gC00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	230 — Glycoprotein D; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2gD00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	230 — Glycoprotein D; Chain: A;
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	131.416 Å
Unit-cell length b length_b	131.416 Å
Unit-cell length c length_c	83.265 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 4
Space-group number int_tables_number	75
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2830
R_work r_work	0.2780
R_free r_free	0.2970

Description description	Glycoprotein D
Molecular weight formula_weight	31837.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,C
Atom count atom_count	15376

Structure of a C-terminally truncated form of glycoprotein D from HSV-1

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

Glycoprotein D

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

1l2g__assembly_4__model_2

1l2g__assembly_4__model_2 | I(q)

1l2g__assembly_4__model_2 | 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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Source organism organism	Human herpesvirus 1
Common name common_name	Herpes simplex virus type 1
NCBI taxonomy ID ncbi_taxonomy_id	10298
Host organism host_organism	Spodoptera frugiperda

Structure of a C-terminally truncated form of glycoprotein D from HSV-1

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

Glycoprotein D

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

1l2g__assembly_4__model_2

1l2g__assembly_4__model_2 | I(q)

1l2g__assembly_4__model_2 | 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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)