9ok9

Crystal structure of an MKP5 allosteric loop mutant, P447V, in complex with an allosteric inhibitor

Method: X-RAY DIFFRACTION Dmax: 95.6 Å Quality: REASONABLE

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

Dual specificity protein phosphatase 10

Homo sapiens

UniProt Q9Y6W6

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 320–467 Fragment:UNP residues 320-467 Mutation:P447V CJA 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;297 K;0.2 M ADA, pH 6.7 (buffer), 20% w/v PEG4000 (precipitant) Resolution 3.00 Å R-free 0.239
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 320–467 Fragment:UNP residues 320-467 Mutation:P447V CJA 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;297 K;0.2 M ADA, pH 6.7 (buffer), 20% w/v PEG4000 (precipitant) Resolution 3.00 Å R-free 0.239
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 320–467 Fragment:UNP residues 320-467 Mutation:P447V CJA 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;297 K;0.2 M ADA, pH 6.7 (buffer), 20% w/v PEG4000 (precipitant) Resolution 3.00 Å R-free 0.239
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 320–467 Fragment:UNP residues 320-467 Mutation:P447V CJA 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;297 K;0.2 M ADA, pH 6.7 (buffer), 20% w/v PEG4000 (precipitant) Resolution 3.00 Å R-free 0.239
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 320–467 Fragment:UNP residues 320-467 Mutation:P447V CJA 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;297 K;0.2 M ADA, pH 6.7 (buffer), 20% w/v PEG4000 (precipitant) Resolution 3.00 Å R-free 0.239
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 320–467 Fragment:UNP residues 320-467 Mutation:P447V CJA 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;297 K;0.2 M ADA, pH 6.7 (buffer), 20% w/v PEG4000 (precipitant) Resolution 3.00 Å R-free 0.239

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.

22 other PDB entries and 96 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DUS10_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–149; UniProt 320–467 Author chain B; PDBConstruct 2–149; UniProt 320–467 Author chain C; PDBConstruct 2–149; UniProt 320–467 Author chain D; PDBConstruct 2–149; UniProt 320–467 Author chain E; PDBConstruct 2–149; UniProt 320–467 Author chain F; PDBConstruct 2–149; UniProt 320–467

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 9ok9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ok9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ok9
Deposition date deposition_date2025-05-09
最后修订 last_revision2025-07-30
Structure title titleCrystal structure of an MKP5 allosteric loop mutant, P447V, in complex with an allosteric inhibitor
Keywords keywordsallosteric site, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.76
Radius of gyration Rg (electron density) rg_electron30.78
Forward intensity I(0) i0159527000.00
Molecular weight molecular_weight102890.0 kDa
Excluded volume excluded_volume129660 ų
Envelope volume envelope_volume161070 ų
Hydration-shell volume shell_volume42990 ų
Envelope diameter envelope_diameter98.1
Shell Rg shell_rg38.45
Envelope Rg envelope_rg30.37
Shape Rg shape_rg30.78
Total Rg total_rg31.44
Total atoms total_atoms7231
Residues n_residues884
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 dmax95.6
Rg (real space) rg_real31.52
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real1.5950e+08
I(0) uncertainty (real space) i0_real_error2.1920e+06
Rg (reciprocal space) rg_reciprocal31.63
I(0) (reciprocal space) i0_reciprocal159500000.0000
Solution quality estimate total_estimate0.7154
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.0
Skewness Skewness skewness0.048
Kurtosis Kurtosis kurtosis-0.567
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35130000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.984; Smooth: 0.954

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)