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- PDB-9nsb: Crystal structure of an MKP5 allosteric loop mutant, S446G, in co... -

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Basic information

Entry
Database: PDB / ID: 9nsb
TitleCrystal structure of an MKP5 allosteric loop mutant, S446G, 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 MAPK pathway / negative regulation of epithelial cell proliferation / response to lipopolysaccharide / signal transduction / nucleoplasm / nucleus / cytosol / cytoplasm
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 / Tyrosine specific protein phosphatases domain profile. / 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: 2.5 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
DepositionMar 16, 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)104,83312
Polymers102,6466
Non-polymers2,1876
Water00
1
A: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4722
Polymers17,1081
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)17,4722
Polymers17,1081
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)17,4722
Polymers17,1081
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)17,4722
Polymers17,1081
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)17,4722
Polymers17,1081
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)17,4722
Polymers17,1081
Non-polymers3651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.697, 99.559, 135.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 17107.633 Da / Num. of mol.: 6 / Fragment: UNP residues 320-466 / Mutation: S446G
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
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: 3.14 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Tricine, pH 7.4, sodium hydroxide, PEG4000

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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: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.5→34.5 Å / Num. obs: 45398 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 52.14 Å2 / CC1/2: 0.99 / Net I/σ(I): 11.89
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.1714 / Num. unique obs: 4478 / CC1/2: 0.641

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→34.5 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 2368 5.22 %
Rwork0.2106 --
obs0.2133 45376 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6963 0 138 0 7101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167286
X-RAY DIFFRACTIONf_angle_d1.6589892
X-RAY DIFFRACTIONf_dihedral_angle_d11.411070
X-RAY DIFFRACTIONf_chiral_restr0.0771079
X-RAY DIFFRACTIONf_plane_restr0.0141281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.41781440.37972499X-RAY DIFFRACTION100
2.55-2.610.48431190.35592488X-RAY DIFFRACTION100
2.61-2.670.3961380.31912505X-RAY DIFFRACTION100
2.67-2.730.35931620.29992468X-RAY DIFFRACTION100
2.73-2.810.3131430.27232483X-RAY DIFFRACTION100
2.81-2.890.40681230.27982525X-RAY DIFFRACTION100
2.89-2.980.38711200.27862515X-RAY DIFFRACTION100
2.98-3.090.3031490.2842505X-RAY DIFFRACTION100
3.09-3.210.28361360.25542513X-RAY DIFFRACTION100
3.21-3.360.3041260.22982519X-RAY DIFFRACTION100
3.36-3.540.28421500.22062536X-RAY DIFFRACTION100
3.54-3.760.29911540.20282494X-RAY DIFFRACTION100
3.76-4.050.22421470.18312526X-RAY DIFFRACTION100
4.05-4.450.20661420.1542538X-RAY DIFFRACTION100
4.45-5.10.19861510.15232563X-RAY DIFFRACTION100
5.1-6.410.23511290.20012604X-RAY DIFFRACTION100
6.42-34.50.19291350.17552727X-RAY DIFFRACTION100

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