SAXSdb — 6wer

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

Non-structural protein 1

Dengue virus 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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 775–1127 Chain B； UniProt 775–1127	Not recorded	2B7 Fab heavy chain × 2 2B7 Fab light chain × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.2；293 K；23% PEG 3350, 0.25 M MgCl2, 0.1 M sodium acetate pH 5.2	Resolution 3.96 Å R-free 0.311

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 6WER	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J35 Cryo-EM reconstruction of Dengue virus at 37 C Deposited 2013-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer NTE；pH 7.3；NTE cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger.	Resolution 35.00 Å
3J35 Cryo-EM reconstruction of Dengue virus at 37 C Deposited 2013-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer NTE；pH 7.3；NTE cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger.	Resolution 35.00 Å
3J35 Cryo-EM reconstruction of Dengue virus at 37 C Deposited 2013-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer NTE；pH 7.3；NTE cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger.	Resolution 35.00 Å
3J35 Cryo-EM reconstruction of Dengue virus at 37 C Deposited 2013-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer NTE；pH 7.3；NTE cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger.	Resolution 35.00 Å
3J35 Cryo-EM reconstruction of Dengue virus at 37 C Deposited 2013-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer NTE；pH 7.3；NTE cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger.	Resolution 35.00 Å
6WY1 Crystal structure of an engineered thermostable dengue virus 2 envelope protein dimer Deposited 2020-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 281–677（397 aa）	Mutation：G106D, A259W, T262R, F279W, T280P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；296 K；15% PEG 3350 pH 4.4, 0.1M Sodium Acetate Trihydrate + 0.1M Sodium Iodide	Resolution 3.42 Å R-free 0.337
6ZQU Cryo-EM structure of mature Dengue virus 2 at 3.1 angstrom resolution Deposited 2020-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 360 PDB declaration: 360-meric	Chain A 281–775（495 aa） Chain C 281–775（495 aa） Chain E 281–775（495 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 360	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；PBS buffer cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 Å
7K93 DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv) Deposited 2020-09-28	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 775–1127（353 aa） Chain B 775–1127（353 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；50 mM Tris pH 8.5, 50 mM (NH4)2SO4, 10% (v/v) glycerol	Resolution 2.89 Å R-free 0.269
7K93 DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv) Deposited 2020-09-28	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 775–1127（353 aa） Chain D 775–1127（353 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；50 mM Tris pH 8.5, 50 mM (NH4)2SO4, 10% (v/v) glycerol	Resolution 2.89 Å R-free 0.269

4 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	D0EPS0_9FLAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–376； UniProt 775–1127 Author chain B； PDBConstruct 24–376； UniProt 775–1127

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	6wer
Deposition date deposition_date	2020-04-02
Structure title title	DENV2 NS1 in complex with neutralizing 2B7 Fab fragment
Keywords keywords	Flavivirus NS1, Antibody, Fab fragment, 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	53.46 Å
Radius of gyration Rg (electron density) rg_electron	54.32 Å
Forward intensity I(0) i0	426591000.00
Molecular weight molecular_weight	166850.0 kDa
Excluded volume excluded_volume	207110 Å³
Envelope volume envelope_volume	301990 Å³
Hydration-shell volume shell_volume	52448 Å³
Envelope diameter envelope_diameter	191.5 Å
Shell Rg shell_rg	47.49 Å
Envelope Rg envelope_rg	54.76 Å
Shape Rg shape_rg	54.33 Å
Total Rg total_rg	54.02 Å
Total atoms total_atoms	11710
Residues n_residues	1504
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	185.8 Å
Rg (real space) rg_real	56.26 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	4.2840e+08
I(0) uncertainty (real space) i0_real_error	7.1540e+06
Rg (reciprocal space) rg_reciprocal	52.83 Å
I(0) (reciprocal space) i0_reciprocal	425800000.0000
Solution quality estimate total_estimate	0.5612
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.5 Å
Skewness Skewness skewness	0.603
Kurtosis Kurtosis kurtosis	-0.399
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	1.6290
Highest regularization parameter α highest_alpha	24870000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.628; Stabil: 0.916; Sysdev: 0.000; Positv: 1.000; Valcen: 0.572; Smooth: 0.097

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Non-structural protein 1
Molecular weight formula_weight	42674.2 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	11710

AHHHHHHSSGVDLGTENLYFQSNADSGCVVSWKNKELKCGSGIFITDNVHTWTEQYKFQPESPSKLASAIQKAHEEGICGIRSVTRLENLMWKQITPELNHILSENEVKLTIMTGDIKGIMQAGKRSLRPQPTELKYSWKTWGKAKMLSTESHNQTFLIDGPETAECPNTNRAWNSLEVEDYGFGVFTTNIWLKLKEKQDVFCDSKLMSAAIKDNRAVHADMGYWIESALNDTWKIEKASFIEVKNCHWPKSHTLWSNGVLESEMIIPKNLAGPVSQHNYRPGYHTQITGPWHLGKLEMDFDFCDGTTVVVTEDCGNRGPSLRTTTASGKLITEWCCRSCTLPPLRYRGEDGCWYGMEIRPLKEKEENLVNSLVTA

来源 Source

来源生物 organism	Dengue virus 2
NCBI Class编号 ncbi_taxonomy_id	11060
宿主生物 host_organism	unidentified baculovirus

Entity 2 Entity 2 polymer

Description description	2B7 Fab heavy chain
Molecular weight formula_weight	28651.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E

MEWSWIFLFLLSGTAGVHSEVQLQQSGPELVKPGASVKMSCKASGCTLTNCFMHWMKQKPGQDLEWIGYINPYNDMTKYSENFKGKATLTSDKSSSTAFMELSSLTSEDSAVYYCARGYLLRTGCFDYWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPNLEGGPSV

Entity 3 Entity 3 polymer

Description description	2B7 Fab light chain
Molecular weight formula_weight	26204.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F

METDTLLLWVLLLWVPGSTGNIVLTQSPASLAVSLGQRATISCRASESVDSYGYSFMHWYQQKPGQPPKVLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNENPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	148.465 Å
Unit-cell length b length_b	148.465 Å
Unit-cell length c length_c	517.050 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	32

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	tetragonal

Resolution resolution	3.960 Å
Low-resolution limit resolution_low	29.800 Å
R factor r_factor	0.2773
R_work r_work	0.2756
R_free r_free	0.3113

fit	/app/data/saxs_computation/we/6wer/6wer.fit
pddf	/app/data/pr_computation/we/6wer/6wer.pr.out
profile	/app/data/saxs_computation/we/6wer/6wer.dat

DENV2 NS1 in complex with neutralizing 2B7 Fab fragment

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

Non-structural protein 1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)