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- PDB-2gtm: Mutated Mouse P38 MAP Kinase Domain in complex with Inhibitor PG-... -

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Basic information

Entry
Database: PDB / ID: 2gtm
TitleMutated Mouse P38 MAP Kinase Domain in complex with Inhibitor PG-892579
ComponentsMitogen-activated protein kinase 14
KeywordsTRANSFERASE / MAP KINASE P38 / P38
Function / homology
Function and homology information


p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / Regulation of MITF-M-dependent genes involved in pigmentation / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence ...p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / Regulation of MITF-M-dependent genes involved in pigmentation / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Myogenesis / VEGFA-VEGFR2 Pathway / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / cartilage condensation / positive regulation of myoblast fusion / cellular response to UV-B / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / D-glucose import / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / negative regulation of hippo signaling / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / striated muscle cell differentiation / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / Neutrophil degranulation / positive regulation of erythrocyte differentiation / osteoclast differentiation / DNA damage checkpoint signaling / positive regulation of D-glucose import / stem cell differentiation / cellular response to ionizing radiation / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / placenta development / cellular response to virus / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / MAPK cascade / cellular response to tumor necrosis factor / kinase activity / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / angiogenesis / response to lipopolysaccharide / transcription by RNA polymerase II / protein kinase activity / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / glutamatergic synapse / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain ...Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-LID / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWalter, R.L. / Mekel, M.J. / Evdokimov, A.G. / Pokross, M.E. / Sabat, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: The development of novel C-2, C-8, and N-9 trisubstituted purines as inhibitors of TNF-alpha production.
Authors: Sabat, M. / Vanrens, J.C. / Clark, M.P. / Brugel, T.A. / Maier, J. / Bookland, R.G. / Laufersweiler, M.J. / Laughlin, S.K. / Golebiowski, A. / De, B. / Hsieh, L.C. / Walter, R.L. / Mekel, M.J. / Janusz, M.J.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3012
Polymers39,9011
Non-polymers4011
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.876, 73.627, 76.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase 14 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / CRK1


Mass: 39900.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P47811, mitogen-activated protein kinase
#2: Chemical ChemComp-LID / 8-(2-CHLOROPHENYLAMINO)-2-(2,6-DIFLUOROPHENYLAMINO)-9-ETHYL-9H-PURINE-1,7-DIIUM / 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


Mass: 400.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15ClF2N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18%(W/V) PEG 1500, 0.1M MES (pH 6.5), streak seed, 1-3 days to maximum size, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 10.2 / Number: 133433 / Rmerge(I) obs: 0.051 / Χ2: 0.92 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 27976 / % possible obs: 97
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.095099.410.0291.279
3.254.0910010.0321.043
2.843.2510010.0480.86
2.582.8410010.0750.895
2.392.5899.910.1170.926
2.252.3999.910.1520.889
2.142.2599.810.1950.85
2.052.1498.210.2630.839
1.972.0590.410.330.808
1.91.9781.610.4470.813
ReflectionResolution: 1.9→50 Å / Num. all: 29034 / Num. obs: 27929 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.045 / Χ2: 0.92 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.970.44723040.81381.6
1.97-2.050.3325690.80890.4
2.05-2.140.26327810.83998.2
2.14-2.250.19528590.8599.8
2.25-2.390.15228270.88999.9
2.39-2.580.11728760.92699.9
2.58-2.840.07528640.895100
2.84-3.250.04828980.86100
3.25-4.090.03229311.043100
4.09-500.02930671.27999.4

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Phasing

Phasing MRRfactor: 0.482 / Cor.coef. Fo:Fc: 0.509 / Cor.coef. Io to Ic: 0.204
Highest resolutionLowest resolution
Rotation3 Å52.705 Å
Translation3 Å52.705 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345data collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In house

Resolution: 1.9→40.8 Å / Cross valid method: R-free / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.261 1323 5% random
Rwork0.212 --
all0.231 29034 -
obs0.214 27323 -
Displacement parametersBiso mean: 39.005 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 28 170 2954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.978
X-RAY DIFFRACTIONr_bond_refined_d0.023
X-RAY DIFFRACTIONr_chiral_restr0.143

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