7h9h

Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z55692894 (CHIKV_MacB-x1444)

Method: X-RAY DIFFRACTION Dmax: 95.1 Å Quality: EXCELLENT

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

Non-structural protein 3

Chikungunya virus

UniProt Q8JUX6

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1334–1493 Fragment:macrodomain DMS DIMETHYL SULFOXIDE × 7 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 3 8P7 2-methyl-1~{H}-benzimidazole × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;293.15 K;0.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad Resolution 1.54 Å R-free 0.225
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1334–1493 Fragment:macrodomain DMS DIMETHYL SULFOXIDE × 3 CL CHLORIDE ION × 3 8P7 2-methyl-1~{H}-benzimidazole × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;293.15 K;0.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad Resolution 1.54 Å R-free 0.225
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1334–1493 Fragment:macrodomain DMS DIMETHYL SULFOXIDE × 4 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;293.15 K;0.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad Resolution 1.54 Å R-free 0.225
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1334–1493 Fragment:macrodomain DMS DIMETHYL SULFOXIDE × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 2 8P7 2-methyl-1~{H}-benzimidazole × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;293.15 K;0.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad Resolution 1.54 Å R-free 0.225

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.

163 other PDB entries and 601 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLN_CHIKS
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–163; UniProt 1334–1493 Author chain B; PDBConstruct 4–163; UniProt 1334–1493 Author chain C; PDBConstruct 4–163; UniProt 1334–1493 Author chain D; PDBConstruct 4–163; UniProt 1334–1493

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 7h9h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7h9h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7h9h
Deposition date deposition_date2024-04-26
最后修订 last_revision2024-05-29
Structure title titleGroup deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z55692894 (CHIKV_MacB-x1444)
Keywords keywordsDiamond Light Source, I04-1, READDI, Chikungunya Virus, crystallographic fragment screening, PanDDA, XChemExplorer, 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_guinier30.01
Radius of gyration Rg (electron density) rg_electron29.20
Forward intensity I(0) i092568400.00
Molecular weight molecular_weight73182.0 kDa
Excluded volume excluded_volume90587 ų
Envelope volume envelope_volume115160 ų
Hydration-shell volume shell_volume33192 ų
Envelope diameter envelope_diameter100.0
Shell Rg shell_rg36.07
Envelope Rg envelope_rg28.83
Shape Rg shape_rg29.20
Total Rg total_rg29.84
Total atoms total_atoms5086
Residues n_residues648
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 dmax95.1
Rg (real space) rg_real29.95
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real9.2570e+07
I(0) uncertainty (real space) i0_real_error1.2260e+06
Rg (reciprocal space) rg_reciprocal29.98
I(0) (reciprocal space) i0_reciprocal92570000.0000
Solution quality estimate total_estimate0.9035
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.0
Skewness Skewness skewness0.194
Kurtosis Kurtosis kurtosis-0.588
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38890000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.948

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)