SAXSdb — 5yvw

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

Genome polyprotein

Dengue virus 4

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1393–1439 Chain B； UniProt 1494–2092	Mutation：S135A	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M HEPES pH 7.0, 10% PEG 4000	Resolution 3.10 Å R-free 0.251

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 5YVW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YVJ Crystal structure of full length NS2B47-NS3 (gD4NS2BNS3) from Dengue virus 4 in open conformation Deposited 2017-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1475–2092（618 aa） Fragment：UNP residues 1475-2092	Mutation：S135A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；0.1M MES pH7.5, 15% PEG 6000	Resolution 2.51 Å R-free 0.246
5YVU Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain Deposited 2017-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1393–1439（47 aa） Fragment：UNP residues 1393-1439 Chain B 1475–2092（618 aa） Fragment：UNP residues 1475-2092	Mutation：S135A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M MES pH 6.4, 12% PEG6000	Resolution 2.49 Å R-free 0.266
5YVV Crystal structure of full length NS3 protein (gD4NS2BNS3) from DENV4 in closed conformation Deposited 2017-11-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1393–1439（47 aa） Fragment：UNP residues 1393-1439 Chain B 1494–2092（599 aa） Fragment：UNP residues 1494-2092	Mutation：L30S,F31S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M MES pH 6.5, 12% PEG6000	Resolution 3.10 Å R-free 0.279
5YVY Crystal structure of unlinked full length NS3 protein (eD4NS2BNS3) from DENV4 in closed conformation Deposited 2017-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1475–2092（618 aa）	Mutation：L30S,F31S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M MES pH 6.4, 10% PEG 6000	Resolution 3.20 Å R-free 0.257
5YW1 Crystal structure of full length NS3 protein (eD4NS2BNS3) in complex with Bovine Pancreatic Trypsin Inhibitor Deposited 2017-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1475–2092（618 aa） Fragment：UNP residues 1475-2092	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M MES pH 6.0, 12% PEG4000	Resolution 2.60 Å R-free 0.240

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

View Construct and Data Evidence

UniProt name	F8TEL4_9FLAV
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain B； PDBConstruct 1–599； UniProt 1494–2092 Author chain A； PDBConstruct 1–47； UniProt 1393–1439

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	5yvw
Deposition date deposition_date	2017-11-27
Structure title title	Crystal structure of full length NS3 protein (eD4NS2BNS3) from DENV4 in closed conformation
Keywords keywords	SERINE PROTEASE, NON-STRUCTURAL PROTEIN 3, DEAH HELICASE, ATPASE, DENGUE VIRUS, FLAVIVIRUS, 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	30.08 Å
Radius of gyration Rg (electron density) rg_electron	29.68 Å
Forward intensity I(0) i0	74639700.00
Molecular weight molecular_weight	67129.0 kDa
Excluded volume excluded_volume	83693 Å³
Envelope volume envelope_volume	109180 Å³
Hydration-shell volume shell_volume	32389 Å³
Envelope diameter envelope_diameter	107.8 Å
Shell Rg shell_rg	34.82 Å
Envelope Rg envelope_rg	29.86 Å
Shape Rg shape_rg	29.70 Å
Total Rg total_rg	30.12 Å
Total atoms total_atoms	4729
Residues n_residues	621
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	103.1 Å
Rg (real space) rg_real	30.29 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	7.4640e+07
I(0) uncertainty (real space) i0_real_error	1.1760e+06
Rg (reciprocal space) rg_reciprocal	30.20 Å
I(0) (reciprocal space) i0_reciprocal	74630000.0000
Solution quality estimate total_estimate	0.8505
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.554
Kurtosis Kurtosis kurtosis	-0.098
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	32750000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.859

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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	Genome polyprotein
Molecular weight formula_weight	67618.2 kDa
Mutation mutation	S135A
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	4742

EGVYRIMQRGLFGKTQVGVGIHMEGVFHTMWHVTRGSVICHETGRLEPSWADVRNDMISYGGGWRLGDKWDKEEDVQVLAIEPGKNPKHVQTKPGLFKTLTGEIGAVTLDFKPGTAGSPIINKKGKVIGLYGNGVVTKSGDYVSAITQAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPAVKSEHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFMTATPPGSIDPFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKKVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFRLRGEQRKTFVELMRRGDLPVWLSYKVASAGISYKDREWCFTGERNNQILEENMEVEIWTREGEKKKLRPKWLDARVYADPMALKDFKEFASGRK

来源 Source

来源生物 organism	Dengue virus 4
NCBI Class编号 ncbi_taxonomy_id	11070
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	5201.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

ADLSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMI

来源 Source

来源生物 organism	Dengue virus 4
NCBI Class编号 ncbi_taxonomy_id	11070
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5yvwB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5yvwB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	52.770 Å
Unit-cell length b length_b	88.300 Å
Unit-cell length c length_c	81.110 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	45.270 Å
R factor r_factor	0.2094
R_work r_work	0.2072
R_free r_free	0.2505

fit	/app/data/saxs_computation/yv/5yvw/5yvw.fit
pddf	/app/data/pr_computation/yv/5yvw/5yvw.pr.out
profile	/app/data/saxs_computation/yv/5yvw/5yvw.dat

Crystal structure of full length NS3 protein (eD4NS2BNS3) from DENV4 in closed conformation

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

Genome polyprotein

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

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)