SAXSdb — 7k93

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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 775–1127 Chain B； UniProt 775–1127	Not recorded	2B7 single chain fab variable region × 2 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 775–1127 Chain D； UniProt 775–1127	Not recorded	2B7 single chain fab variable region × 2 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

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 7K93	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
6WER DENV2 NS1 in complex with neutralizing 2B7 Fab fragment Deposited 2020-04-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	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 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
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

4 other PDB entries and 8 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 Author chain C； PDBConstruct 24–376； UniProt 775–1127 Author chain D； 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	7k93
Deposition date deposition_date	2020-09-28
Structure title title	DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv)
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	45.31 Å
Radius of gyration Rg (electron density) rg_electron	44.82 Å
Forward intensity I(0) i0	957699000.00
Molecular weight molecular_weight	250620.0 kDa
Excluded volume excluded_volume	311120 Å³
Envelope volume envelope_volume	431000 Å³
Hydration-shell volume shell_volume	78598 Å³
Envelope diameter envelope_diameter	161.0 Å
Shell Rg shell_rg	51.60 Å
Envelope Rg envelope_rg	43.43 Å
Shape Rg shape_rg	44.80 Å
Total Rg total_rg	45.17 Å
Total atoms total_atoms	17581
Residues n_residues	2244
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	148.9 Å
Rg (real space) rg_real	45.15 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	9.5770e+08
I(0) uncertainty (real space) i0_real_error	1.5540e+07
Rg (reciprocal space) rg_reciprocal	45.31 Å
I(0) (reciprocal space) i0_reciprocal	957900000.0000
Solution quality estimate total_estimate	0.8913
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	55.3 Å
Skewness Skewness skewness	0.201
Kurtosis Kurtosis kurtosis	-0.422
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	55120000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.907

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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	Non-structural protein 1
Molecular weight formula_weight	42674.2 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17581

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 single chain fab variable region
Molecular weight formula_weight	26719.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G,I,K

SNAEVQLQQSGPELVKPGASVKMSCKASGCTLTNCFMHWMKQKPGQDLEWIGYINPYNDMTKYSENFKGKATLTSDKSSSTAFMELSSLTSEDSAVYYCARGYLLRTGCFDYWGQGTTLTVSSGGSGGGSGGGSGGGSGGNIVLTQSPASLAVSLGQRATISCRASESVDSYGYSFMHWYQQKPGQPPKVLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNENPLTFGAGTKLELK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d7k93e1
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.1.1.0 — automated matches

Domain ID domain_id	d7k93e2
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.1.1.0 — automated matches

Domain ID domain_id	d7k93g1
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.1.1.0 — automated matches

Domain ID domain_id	d7k93g2
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.1.1.0 — automated matches

Domain ID domain_id	d7k93i1
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.1.1.0 — automated matches

Domain ID domain_id	d7k93i2
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.1.1.0 — automated matches

Domain ID domain_id	d7k93k1
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.1.1.0 — automated matches

Domain ID domain_id	d7k93k2
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.1.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	7k93E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7k93E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7k93G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7k93G02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7k93I01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7k93I02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7k93K01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7k93K02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	69.627 Å
Unit-cell length b length_b	165.593 Å
Unit-cell length c length_c	258.589 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	47.380 Å
R factor r_factor	0.2244
R_work r_work	0.2227
R_free r_free	0.2686

fit	/app/data/saxs_computation/k9/7k93/7k93.fit
pddf	/app/data/pr_computation/k9/7k93/7k93.pr.out
profile	/app/data/saxs_computation/k9/7k93/7k93.dat

DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv)

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)