2ijo

Crystal Structure of the West Nile virus NS2B-NS3 protease complexed with bovine pancreatic trypsin inhibitor

Method: X-RAY DIFFRACTION Dmax: 65.4 Å Quality: GOOD

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

Polyprotein

West Nile virus

UniProt Q203W3

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 1423–1469 Chain B; UniProt 1506–1689 Fragment:NS2B cofactor domain Fragment:NS3 protease domain Mutation:K104R Pancreatic trypsin inhibitor × 1 (P00974) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;20% PEG 8000, 0.1M TRIS-HCL, 0.2M SODIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.30 Å R-free 0.264

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.

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

View Construct and Data Evidence
UniProt name Q203W3_WNV
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 2–48; UniProt 1423–1469 Author chain B; PDBConstruct 1–184; UniProt 1506–1689

Pancreatic trypsin inhibitor

OrganismNot specified

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 36–93 Not recorded Polyprotein × 1 (Q203W3) Polyprotein × 1 (Q203W3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;20% PEG 8000, 0.1M TRIS-HCL, 0.2M SODIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.30 Å R-free 0.264

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 1–58; UniProt 36–93

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 2ijo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ijo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ijo
Deposition date deposition_date2006-09-29
Structure title titleCrystal Structure of the West Nile virus NS2B-NS3 protease complexed with bovine pancreatic trypsin inhibitor
Keywords keywordsWEST NILE VIRUS, PROTEASE, APROTININ, BPTI, NS2B, NS3, FLAVIVIRUS, serine protease, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.68
Radius of gyration Rg (electron density) rg_electron18.65
Forward intensity I(0) i015776500.00
Molecular weight molecular_weight28842.0 kDa
Excluded volume excluded_volume35621 ų
Envelope volume envelope_volume41556 ų
Hydration-shell volume shell_volume18786 ų
Envelope diameter envelope_diameter64.9
Shell Rg shell_rg24.80
Envelope Rg envelope_rg19.03
Shape Rg shape_rg18.62
Total Rg total_rg19.61
Total atoms total_atoms2023
Residues n_residues265
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 dmax65.4
Rg (real space) rg_real19.61
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real1.5780e+07
I(0) uncertainty (real space) i0_real_error2.0170e+05
Rg (reciprocal space) rg_reciprocal19.62
I(0) (reciprocal space) i0_reciprocal15780000.0000
Solution quality estimate total_estimate0.8837
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9
Skewness Skewness skewness0.262
Kurtosis Kurtosis kurtosis-0.328
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3350000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.980

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2ijoa_
Class classg — Small proteins
Fold Fold foldg.96 — Flavivirus non-structural protein NS2B-like
Superfamily Superfamily superfamilyg.96.1 — Flavivirus non-structural protein NS2B-like
Family Family familyg.96.1.1 — Flavivirus non-structural protein NS2B-like
Domain ID domain_idd2ijob1
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.3 — Viral proteases
Domain ID domain_idd2ijoi_
Class classg — Small proteins
Fold Fold foldg.8 — BPTI-like
Superfamily Superfamily superfamilyg.8.1 — BPTI-like
Family Family familyg.8.1.1 — Small Kunitz-type inhibitors & BPTI-like toxins

CATH v4.4 (3 domains)

Domain ID domain_id2ijoB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily120
Domain ID domain_id2ijoB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2ijoI00
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)