SAXSdb — 1at3

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

HERPES SIMPLEX VIRUS TYPE II PROTEASE

Human herpesvirus 2

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–247 Chain B； UniProt 1–247	Not recorded	DFP DIISOPROPYL PHOSPHONATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；10% PEG4000, PH 5.0	Resolution 2.50 Å R-free 0.291
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–247 Chain B； UniProt 1–247	Not recorded	DFP DIISOPROPYL PHOSPHONATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；10% PEG4000, PH 5.0	Resolution 2.50 Å R-free 0.291

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q69527_HHV2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–247； UniProt 1–247 Author chain B； PDBConstruct 1–247； UniProt 1–247

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	1at3
Deposition date deposition_date	1997-08-16
Structure title title	HERPES SIMPLEX VIRUS TYPE II PROTEASE
Keywords keywords	SERINE PROTEASE, VIRAL PROTEASE, HSV2 PROTEASE; SERINE PROTEASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.50 Å
Radius of gyration Rg (electron density) rg_electron	24.68 Å
Forward intensity I(0) i0	37614800.00
Molecular weight molecular_weight	47049.0 kDa
Excluded volume excluded_volume	58868 Å³
Envelope volume envelope_volume	70534 Å³
Hydration-shell volume shell_volume	24843 Å³
Envelope diameter envelope_diameter	85.1 Å
Shell Rg shell_rg	31.16 Å
Envelope Rg envelope_rg	24.79 Å
Shape Rg shape_rg	24.72 Å
Total Rg total_rg	25.29 Å
Total atoms total_atoms	3313
Residues n_residues	434
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	83.5 Å
Rg (real space) rg_real	25.62 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	3.7610e+07
I(0) uncertainty (real space) i0_real_error	5.5880e+05
Rg (reciprocal space) rg_reciprocal	25.59 Å
I(0) (reciprocal space) i0_reciprocal	37610000.0000
Solution quality estimate total_estimate	0.8673
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.499
Kurtosis Kurtosis kurtosis	-0.313
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17920000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.929

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HERPES SIMPLEX VIRUS TYPE II PROTEASE
Molecular weight formula_weight	27056.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3356

MASAEMRERLEAPLPDRAVPIYVAGFLALYDSGDPGELALDPDTVRAALPPENPLPINVDHRARCEVGRVLAVVNDPRGPFFVGLIACVQLERVLETAASAAIFERRGPALSREERLLYLITNYLPSVSLSTKRRGDEVPPDRTLFAHVALCAIGRRLGTIVTYDTSLDAAIAPFRHLDPATREGVRREAAEAELALAGRTWAPGVEALTHTLLSTAVNNMMLRDRWSLVAERRRQAGIAGHTYLQA

来源 Source

来源生物 organism	Human herpesvirus 2
通用名 common_name	Herpes simplex virus type 2
NCBI Class编号 ncbi_taxonomy_id	10310
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DIISOPROPYL PHOSPHONATE
Molecular weight formula_weight	166.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1at3a_
Class class	b — All beta proteins
Fold Fold fold	b.57 — Herpes virus serine proteinase, assemblin
Superfamily Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
Family Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

Domain ID domain_id	d1at3b_
Class class	b — All beta proteins
Fold Fold fold	b.57 — Herpes virus serine proteinase, assemblin
Superfamily Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
Family Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

CATH v4.4 (2 domains)

Domain ID domain_id	1at3A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

Domain ID domain_id	1at3B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

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8. Citations (1)

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Unit-cell length a length_a	71.720 Å
Unit-cell length b length_b	87.430 Å
Unit-cell length c length_c	77.280 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2910

fit	/app/data/saxs_computation/at/1at3/1at3.fit
pddf	/app/data/pr_computation/at/1at3/1at3.pr.out
profile	/app/data/saxs_computation/at/1at3/1at3.dat

HERPES SIMPLEX VIRUS TYPE II PROTEASE

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

HERPES SIMPLEX VIRUS TYPE II PROTEASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)