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- PDB-9o8w: Crystal structure of an MKP5 mutant, Y435F, in complex with an al... -

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Basic information

Entry
Database: PDB / ID: 9o8w
TitleCrystal structure of an MKP5 mutant, Y435F, in complex with an 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: 2.39 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: Nat Commun / Year: 2025
Title: Dynamic and structural insights into allosteric regulation on MKP5 a dual-specificity phosphatase.
Authors: Skeens, E. / Maschietto, F. / Manjula, R. / Shillingford, S. / Murphy, J. / Lolis, E.J. / Batista, V.S. / Bennett, A.M. / Lisi, G.P.
History
DepositionApr 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)105,29014
Polymers102,9106
Non-polymers2,3798
Water1,53185
1
A: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5162
Polymers17,1521
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5162
Polymers17,1521
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5162
Polymers17,1521
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6123
Polymers17,1521
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5162
Polymers17,1521
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6123
Polymers17,1521
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.131, 95.770, 92.805
Angle α, β, γ (deg.)90.00, 117.39, 90.00
Int Tables number4
Space group name H-MP1211

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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: 17151.686 Da / Num. of mol.: 6 / Mutation: Y435F
Source method: isolated from a genetically manipulated source
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
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: 3.49 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2 M ammonium sulfate (precipitant), 0.1 M HEPES, pH 7.5 (buffer)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.39→33.73 Å / Num. obs: 55524 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.049 / Rrim(I) all: 0.124 / Net I/σ(I): 8.7
Reflection shellResolution: 2.39→2.46 Å / Rmerge(I) obs: 0.937 / Num. unique obs: 4517 / CC1/2: 0.806 / Rpim(I) all: 0.41 / Rrim(I) all: 1.024

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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: 2.39→33.73 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 2838 5.12 %
Rwork0.2171 --
obs0.2189 55456 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7096 0 79 85 7260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067369
X-RAY DIFFRACTIONf_angle_d0.9689991
X-RAY DIFFRACTIONf_dihedral_angle_d8.2051068
X-RAY DIFFRACTIONf_chiral_restr0.0441087
X-RAY DIFFRACTIONf_plane_restr0.0051292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.430.30931250.3022622X-RAY DIFFRACTION100
2.43-2.480.38221250.28152613X-RAY DIFFRACTION100
2.48-2.520.29761390.27532626X-RAY DIFFRACTION100
2.52-2.570.31351540.28032629X-RAY DIFFRACTION100
2.57-2.630.30921210.26272610X-RAY DIFFRACTION100
2.63-2.690.2851330.26682618X-RAY DIFFRACTION100
2.69-2.760.31511390.28332616X-RAY DIFFRACTION100
2.76-2.830.35481310.28772644X-RAY DIFFRACTION100
2.83-2.920.36881590.28632615X-RAY DIFFRACTION100
2.92-3.010.31861760.27462616X-RAY DIFFRACTION100
3.01-3.120.32861540.27492590X-RAY DIFFRACTION100
3.12-3.240.29911290.25722627X-RAY DIFFRACTION100
3.24-3.390.26991370.25112655X-RAY DIFFRACTION100
3.39-3.570.29221440.2262612X-RAY DIFFRACTION100
3.57-3.790.22261350.2052642X-RAY DIFFRACTION100
3.79-4.080.22661620.18712628X-RAY DIFFRACTION100
4.08-4.50.19971160.17152664X-RAY DIFFRACTION100
4.5-5.140.18121810.15912613X-RAY DIFFRACTION100
5.14-6.470.21251500.20872652X-RAY DIFFRACTION100
6.47-33.730.22631280.18392726X-RAY DIFFRACTION100

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