SAXSdb — 9t4p

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

Serine protease subunit NS2B,Serine protease NS3

dengue virus type 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1394–1440 Chain A； UniProt 1476–1660	Mutation：K174Q	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；LFS Eco well C09 0.1M HEPES pH 7, 0.2M Lithium chloride, 20% w/v PEG 6000, 10% v/v Ethylene glycol	Resolution 1.95 Å R-free 0.294

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.

Other PDB	Difference from Current Entry 9T4P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 360 PDB declaration: 360-meric	Chain D 115–195（81 aa） Chain E 115–195（81 aa） Chain F 115–195（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 115–195（81 aa） Chain E 115–195（81 aa） Chain F 115–195（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain D 115–195（81 aa） Chain E 115–195（81 aa） Chain F 115–195（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain D 115–195（81 aa） Chain E 115–195（81 aa） Chain F 115–195（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 115–195（81 aa） Chain E 115–195（81 aa） Chain F 115–195（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.50 Å

1 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POLG_DEN28
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–50； UniProt 1394–1440 Author chain A； PDBConstruct 60–244； UniProt 1476–1660

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	9t4p
Deposition date deposition_date	2025-10-30
最后修订 last_revision	2025-11-12
Structure title title	Dengue 2 Virus NS2B-NS3 protease fusion protein with crystal epitope mutation K174Q
Keywords keywords	protease crystal epitopes, VIRAL PROTEIN; VIRAL PROTEIN
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	17.71 Å
Radius of gyration Rg (electron density) rg_electron	16.51 Å
Forward intensity I(0) i0	8386920.00
Molecular weight molecular_weight	21034.0 kDa
Excluded volume excluded_volume	26306 Å³
Envelope volume envelope_volume	31070 Å³
Hydration-shell volume shell_volume	15855 Å³
Envelope diameter envelope_diameter	65.4 Å
Shell Rg shell_rg	22.63 Å
Envelope Rg envelope_rg	17.03 Å
Shape Rg shape_rg	16.46 Å
Total Rg total_rg	17.70 Å
Total atoms total_atoms	2918
Residues n_residues	196
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	63.8 Å
Rg (real space) rg_real	17.64 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	8.3870e+06
I(0) uncertainty (real space) i0_real_error	1.0740e+05
Rg (reciprocal space) rg_reciprocal	17.65 Å
I(0) (reciprocal space) i0_reciprocal	8387000.0000
Solution quality estimate total_estimate	0.7591
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.292
Kurtosis Kurtosis kurtosis	-0.083
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1983000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.634; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	123.486 Å
Unit-cell length b length_b	45.200 Å
Unit-cell length c length_c	40.460 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	42.148 Å
R factor r_factor	—
R_work r_work	0.2257
R_free r_free	0.2939

Description description	Serine protease subunit NS2B,Serine protease NS3
Molecular weight formula_weight	25949.0 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13
Mutation mutation	K174Q
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2966

Dengue 2 Virus NS2B-NS3 protease fusion protein with crystal epitope mutation K174Q

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

Serine protease subunit NS2B,Serine protease NS3

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	dengue virus type 2
NCBI Class编号 ncbi_taxonomy_id	11060
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

fit	/app/data/saxs_computation/t4/9t4p/9t4p.fit
pddf	/app/data/pr_computation/t4/9t4p/9t4p.pr.out
profile	/app/data/saxs_computation/t4/9t4p/9t4p.dat