SAXSdb — 1jma

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

HERPESVIRUS ENTRY MEDIATOR

Human herpesvirus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	GLYCOPROTEIN D × 1 （P57083） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TR14_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–161； UniProt 39–199

GLYCOPROTEIN D

Homo sapiens

UniProt P57083

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	HERPESVIRUS ENTRY MEDIATOR × 1 （Q92956） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGLD_HSV1P
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–285； 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	1jma
Deposition date deposition_date	2001-07-17
Structure title title	CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM
Keywords keywords	V-type Ig molecule and TNFR superfamily, 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.

1jma__assembly_1__model_1

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

Download this curve (.dat)

1jma__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jma__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.88 Å
Rg (electron density)	24.08 Å
Total Rg	24.93 Å
Atom count	2818
Residues	359
Excluded volume	49954 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jma__assembly_1__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	HERPESVIRUS ENTRY MEDIATOR
Molecular weight formula_weight	17768.0 kDa
Mutation mutation	ECTODOMAIN OF THE FULL PROTEIN
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	2885

LPSCKEDEYPVGSECCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMGLRASRNCSRTENAVCGCSPGHFCIVQDGDHCAACRAYATSSPGQRVQKGGTESQDTLCQNCPPGTFSPNGTLEECQHQTKCSWLVTKAGAGTSSSHHHHHH

Source Source

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

Entity 2 Entity 2 polymer

Description description	GLYCOPROTEIN D
Molecular weight formula_weight	32315.7 kDa
Mutation mutation	C-TERMINAL TRUNCATION AT RESIDUE 285
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

KYALADASLKMADPNRFRGKDLPVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPELSETPNATQPELAPEDPEDSALLEDPVGTHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1jmaa_
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	d1jmab1
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d1jmab2
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

CATH v4.4 (3 domains)

Domain ID domain_id	1jmaA00
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	1jmaB01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	1jmaB02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

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Unit-cell length a length_a	129.154 Å
Unit-cell length b length_b	129.154 Å
Unit-cell length c length_c	80.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2370
R_work r_work	0.2360
R_free r_free	0.2590

CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM

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

HERPESVIRUS ENTRY MEDIATOR

State in the Current Structure

Other States of the Same Protein in the Database

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

1jma__assembly_1__model_1

1jma__assembly_1__model_1 | I(q)

1jma__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)

CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM

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

HERPESVIRUS ENTRY MEDIATOR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

1jma__assembly_1__model_1

1jma__assembly_1__model_1 | I(q)

1jma__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)