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- PDB-9ok9: Crystal structure of an MKP5 allosteric loop mutant, P447V, in co... -

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Basic information

Entry
Database: PDB / ID: 9ok9
TitleCrystal structure of an MKP5 allosteric loop mutant, P447V, in complex with an allosteric inhibitor
ComponentsDual specificity protein phosphatase 10
KeywordsHYDROLASE/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: 3 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 an MKP5 allosteric loop mutant, S446G, in complex with an allosteric inhibitor
Authors: Manjula, R. / Bennett, A.M. / Lolis, E.
History
DepositionMay 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 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)105,20612
Polymers103,0186
Non-polymers2,1876
Water00
1
A: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5342
Polymers17,1701
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)17,5342
Polymers17,1701
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)17,5342
Polymers17,1701
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)17,5342
Polymers17,1701
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)17,5342
Polymers17,1701
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)17,5342
Polymers17,1701
Non-polymers3651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.740, 98.252, 136.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 17169.701 Da / Num. of mol.: 6 / Fragment: UNP residues 320-467 / Mutation: P447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5 / Production host: Escherichia coli (E. coli)
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 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ADA, pH 6.7 (buffer), 20% w/v PEG4000 (precipitant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→34.25 Å / Num. obs: 23966 / % possible obs: 93.3 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.056 / Rrim(I) all: 0.11 / Χ2: 0.98 / Net I/σ(I): 10 / Num. measured all: 89252
Reflection shellResolution: 3→3.18 Å / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 1.03 / Num. measured all: 15696 / Num. unique obs: 4089 / CC1/2: 0.62 / Rpim(I) all: 0.597 / Rrim(I) all: 1.194 / Χ2: 1 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→34.25 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 1168 4.88 %
Rwork0.1952 --
obs0.1974 23912 93.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7093 0 138 0 7231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017393
X-RAY DIFFRACTIONf_angle_d1.39710015
X-RAY DIFFRACTIONf_dihedral_angle_d8.5641070
X-RAY DIFFRACTIONf_chiral_restr0.0661096
X-RAY DIFFRACTIONf_plane_restr0.0081286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.41161430.3452998X-RAY DIFFRACTION100
3.14-3.30.33681440.30853012X-RAY DIFFRACTION100
3.3-3.510.3811330.3072420X-RAY DIFFRACTION81
3.51-3.780.38091150.25042562X-RAY DIFFRACTION84
3.78-4.160.26681320.20042519X-RAY DIFFRACTION83
4.16-4.760.17141550.15883045X-RAY DIFFRACTION100
4.76-5.990.22551580.16833060X-RAY DIFFRACTION99
5.99-34.250.17771880.14443128X-RAY DIFFRACTION98

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