8y9v

ZIKV NS2B/NS3 protease

Method: X-RAY DIFFRACTION Dmax: 79.4 Å Quality: REASONABLE

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

Serine protease subunit NS2B

Zika virus

UniProt H8XX12

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1411–1462 Not recorded Serine protease NS3 × 1 (Q32ZE1) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;300 K;PEG 20% 2000, ammonium sulfate 0.2 M, sodium acetate trihydrate 0.1 M Resolution 1.90 Å R-free 0.248
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1411–1462 Not recorded Serine protease NS3 × 1 (Q32ZE1) DAR-LYS-ORN-ARG × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;300 K;PEG 20% 2000, ammonium sulfate 0.2 M, sodium acetate trihydrate 0.1 M Resolution 1.90 Å R-free 0.248

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.

9 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H8XX12_ZIKV
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–53; UniProt 1411–1462 Author chain C; PDBConstruct 2–53; UniProt 1411–1462

Serine protease NS3

Zika virus

UniProt Q32ZE1

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1516–1668 Not recorded Serine protease subunit NS2B × 1 (H8XX12) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;300 K;PEG 20% 2000, ammonium sulfate 0.2 M, sodium acetate trihydrate 0.1 M Resolution 1.90 Å R-free 0.248
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1511–1671 Not recorded Serine protease subunit NS2B × 1 (H8XX12) DAR-LYS-ORN-ARG × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;300 K;PEG 20% 2000, ammonium sulfate 0.2 M, sodium acetate trihydrate 0.1 M Resolution 1.90 Å R-free 0.248

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.

263 other PDB entries and 301 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_ZIKV
Isoform
PDB entities 2, 3
Chains and sequence ranges Author chain B; PDBConstruct 1–153; UniProt 1516–1668 Author chain D; PDBConstruct 1–161; UniProt 1511–1671

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 8y9v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8y9v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8y9v
Deposition date deposition_date2024-02-07
最后修订 last_revision2024-02-28
Structure title titleZIKV NS2B/NS3 protease
Keywords keywordsZIKV, NS2B/NS3 protease, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.78
Radius of gyration Rg (electron density) rg_electron23.08
Forward intensity I(0) i029516400.00
Molecular weight molecular_weight41224.0 kDa
Excluded volume excluded_volume51452 ų
Envelope volume envelope_volume62657 ų
Hydration-shell volume shell_volume23096 ų
Envelope diameter envelope_diameter81.3
Shell Rg shell_rg29.58
Envelope Rg envelope_rg23.26
Shape Rg shape_rg23.04
Total Rg total_rg23.99
Total atoms total_atoms2904
Residues n_residues385
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 dmax79.4
Rg (real space) rg_real23.80
Rg uncertainty (real space) rg_real_error0.55
I(0) (real space) i0_real2.9520e+07
I(0) uncertainty (real space) i0_real_error4.4280e+05
Rg (reciprocal space) rg_reciprocal23.80
I(0) (reciprocal space) i0_reciprocal29520000.0000
Solution quality estimate total_estimate0.7164
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.8
Skewness Skewness skewness0.371
Kurtosis Kurtosis kurtosis-0.440
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12190000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 0.286; Positv: 1.000; Valcen: 0.943; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)