9q7x

Crystal structure of the MKP5 loop mutant N448A in complex with the allosteric inhibitor

Method: X-RAY DIFFRACTION Dmax: 107.8 Å Quality: EXCELLENT

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 320–466 Not recorded 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;293 K;0.1 M HEPES, pH 7.5, 1.4 M sodium citrate tribasic dihydrate Resolution 2.95 Å R-free 0.241
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 320–466 Not recorded 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;293 K;0.1 M HEPES, pH 7.5, 1.4 M sodium citrate tribasic dihydrate Resolution 2.95 Å R-free 0.241
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 320–466 Not recorded 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;293 K;0.1 M HEPES, pH 7.5, 1.4 M sodium citrate tribasic dihydrate Resolution 2.95 Å R-free 0.241
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 320–466 Not recorded 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;293 K;0.1 M HEPES, pH 7.5, 1.4 M sodium citrate tribasic dihydrate Resolution 2.95 Å R-free 0.241
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 320–466 Not recorded 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;293 K;0.1 M HEPES, pH 7.5, 1.4 M sodium citrate tribasic dihydrate Resolution 2.95 Å R-free 0.241
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 320–466 Not recorded 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;293 K;0.1 M HEPES, pH 7.5, 1.4 M sodium citrate tribasic dihydrate Resolution 2.95 Å R-free 0.241

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 2–148; UniProt 320–466 Author chain B; PDBConstruct 2–148; UniProt 320–466 Author chain C; PDBConstruct 2–148; UniProt 320–466 Author chain D; PDBConstruct 2–148; UniProt 320–466 Author chain E; PDBConstruct 2–148; UniProt 320–466 Author chain F; PDBConstruct 2–148; UniProt 320–466

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 9q7x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9q7x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9q7x
Deposition date deposition_date2025-08-25
最后修订 last_revision2025-09-10
Structure title titleCrystal structure of the MKP5 loop mutant N448A in complex with the allosteric inhibitor
Keywords keywordsMKP5, allosteric inhibitor, allosteric 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_guinier35.13
Radius of gyration Rg (electron density) rg_electron34.51
Forward intensity I(0) i0155559000.00
Molecular weight molecular_weight102700.0 kDa
Excluded volume excluded_volume129460 ų
Envelope volume envelope_volume164880 ų
Hydration-shell volume shell_volume40920 ų
Envelope diameter envelope_diameter109.6
Shell Rg shell_rg40.31
Envelope Rg envelope_rg34.10
Shape Rg shape_rg34.52
Total Rg total_rg34.88
Total atoms total_atoms14328
Residues n_residues882
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 dmax107.8
Rg (real space) rg_real35.01
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real1.5560e+08
I(0) uncertainty (real space) i0_real_error2.4390e+06
Rg (reciprocal space) rg_reciprocal35.09
I(0) (reciprocal space) i0_reciprocal155600000.0000
Solution quality estimate total_estimate0.9095
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.5
Skewness Skewness skewness0.101
Kurtosis Kurtosis kurtosis-0.703
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20060000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.890

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)