5yvu

Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain

Method: X-RAY DIFFRACTION Dmax: 104.2 Å Quality: GOOD

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

Genome polyprotein

Dengue virus 4

UniProt F8TEL4

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1393–1439 Chain B; UniProt 1475–2092 Fragment:UNP residues 1475-2092 Mutation:S135A Fragment:UNP residues 1393-1439 Pancreatic trypsin inhibitor × 1 (P00974) 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

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.

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 10–627; UniProt 1475–2092 Author chain A; PDBConstruct 9–55; UniProt 1393–1439

Pancreatic trypsin inhibitor

Bos taurus

UniProt P00974

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain I; UniProt 36–90 Fragment:UNP residues 36-90 Genome polyprotein × 1 (F8TEL4) Genome polyprotein × 1 (F8TEL4) 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

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.

123 other PDB entries and 265 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BPT1_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain I; PDBConstruct 1–55; UniProt 36–90

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5yvu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5yvu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5yvu
Deposition date deposition_date2017-11-27
Structure title titleCrystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain
Keywords keywordsSERINE PROTEASE, NON-STRUCTURAL PROTEIN 3, DEAH HELICASE, FLAVIVIRUS, DENGUE, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.13
Radius of gyration Rg (electron density) rg_electron30.72
Forward intensity I(0) i093580500.00
Molecular weight molecular_weight75327.0 kDa
Excluded volume excluded_volume93784 ų
Envelope volume envelope_volume121940 ų
Hydration-shell volume shell_volume34406 ų
Envelope diameter envelope_diameter104.9
Shell Rg shell_rg36.47
Envelope Rg envelope_rg30.59
Shape Rg shape_rg30.71
Total Rg total_rg31.25
Total atoms total_atoms5302
Residues n_residues694
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax104.2
Rg (real space) rg_real31.25
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real9.3580e+07
I(0) uncertainty (real space) i0_real_error1.3420e+06
Rg (reciprocal space) rg_reciprocal31.20
I(0) (reciprocal space) i0_reciprocal93580000.0000
Solution quality estimate total_estimate0.8730
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary32.7
Skewness Skewness skewness0.428
Kurtosis Kurtosis kurtosis-0.382
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26230000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.882

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5yvui_
Class classg — Small proteins
Fold Fold foldg.8 — BPTI-like
Superfamily Superfamily superfamilyg.8.1 — BPTI-like
Family Family familyg.8.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id5yvuB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5yvuB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5yvuI00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain

8. Citations (1)

9. Files and Curves (10)