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- PDB-9q7x: Crystal structure of the MKP5 loop mutant N448A in complex with t... -

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Basic information

Entry
Database: PDB / ID: 9q7x
TitleCrystal structure of the MKP5 loop mutant N448A in complex with the allosteric inhibitor
ComponentsDual specificity protein phosphatase 10
KeywordsHYDROLASE/INHIBITOR / MKP5 / allosteric inhibitor / allosteric site / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / regulation of brown fat cell differentiation / negative regulation of epithelial cell migration / negative regulation of p38MAPK cascade / negative regulation of oligodendrocyte differentiation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / regulation of brown fat cell differentiation / negative regulation of epithelial cell migration / negative regulation of p38MAPK cascade / negative regulation of oligodendrocyte differentiation / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / JUN kinase binding / dephosphorylation / negative regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / positive regulation of regulatory T cell differentiation / mitogen-activated protein kinase p38 binding / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphatase activity / oligodendrocyte differentiation / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / protein-tyrosine-phosphatase / negative regulation of cell migration / negative regulation of ERK1 and ERK2 cascade / negative regulation of epithelial cell proliferation / Negative regulation of MAPK pathway / response to lipopolysaccharide / signal transduction / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Chem-CJA / Dual specificity protein phosphatase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsManjula, R. / Bennett, A.M. / Lolis, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)RO1 HL158876 United States
CitationJournal: To Be Published
Title: Crystal structure of the MKP5 loop mutant N448A in complex with the allosteric inhibitor
Authors: Manjula, R. / Bennett, A.M. / Lolis, E.
History
DepositionAug 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 10
B: Dual specificity protein phosphatase 10
C: Dual specificity protein phosphatase 10
D: Dual specificity protein phosphatase 10
E: Dual specificity protein phosphatase 10
F: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,32912
Polymers102,1416
Non-polymers2,1876
Water00
1
A: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3882
Polymers17,0241
Non-polymers3651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3882
Polymers17,0241
Non-polymers3651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3882
Polymers17,0241
Non-polymers3651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3882
Polymers17,0241
Non-polymers3651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3882
Polymers17,0241
Non-polymers3651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3882
Polymers17,0241
Non-polymers3651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.860, 129.950, 84.010
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z

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Components

#1: Protein
Dual specificity protein phosphatase 10 / Mitogen-activated protein kinase phosphatase 5 / MAP kinase phosphatase 5 / MKP-5


Mass: 17023.559 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Catalytic domain with a mutation at Asn448 / Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-CJA / 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one


Mass: 364.549 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H20N2OS3
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 1.4 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.95→65.84 Å / Num. obs: 28449 / % possible obs: 95.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 56.04 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.154 / Net I/σ(I): 8.6
Reflection shellResolution: 2.95→3.13 Å / Rmerge(I) obs: 0.714 / Num. unique obs: 4821 / CC1/2: 0.567

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→65.84 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1480 5.22 %
Rwork0.1813 --
obs0.1845 28356 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→65.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7080 0 138 0 7218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047398
X-RAY DIFFRACTIONf_angle_d0.77410022
X-RAY DIFFRACTIONf_dihedral_angle_d22.0342806
X-RAY DIFFRACTIONf_chiral_restr0.041087
X-RAY DIFFRACTIONf_plane_restr0.0061290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.050.35271520.27282535X-RAY DIFFRACTION100
3.05-3.150.30651510.25722566X-RAY DIFFRACTION100
3.15-3.280.32651260.23362535X-RAY DIFFRACTION99
3.28-3.430.28891300.2232555X-RAY DIFFRACTION100
3.43-3.610.29021070.20292046X-RAY DIFFRACTION79
3.61-3.840.27351160.20582147X-RAY DIFFRACTION84
3.84-4.130.23841100.16242206X-RAY DIFFRACTION86
4.13-4.550.1951410.14532559X-RAY DIFFRACTION100
4.55-5.210.21871260.14012581X-RAY DIFFRACTION100
5.21-6.560.22811670.17342566X-RAY DIFFRACTION100
6.56-65.840.16131540.14752580X-RAY DIFFRACTION99

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