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- PDB-6qe1: P38 alpha complex with AR117046 -

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Basic information

Entry
Database: PDB / ID: 6qe1
TitleP38 alpha complex with AR117046
ComponentsMitogen-activated protein kinase 14
KeywordsSIGNALING PROTEIN / Inhibitor / Complex / Kinase
Function / homology
Function and homology information


stress-activated protein kinase signaling cascade / positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / CD163 mediating an anti-inflammatory response / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / positive regulation of myoblast fusion / KSRP (KHSRP) binds and destabilizes mRNA ...stress-activated protein kinase signaling cascade / positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / CD163 mediating an anti-inflammatory response / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / positive regulation of myoblast fusion / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation / cellular response to UV-B / positive regulation of muscle cell differentiation / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / Myogenesis / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / D-glucose import / Activation of the AP-1 family of transcription factors / p38MAPK cascade / ERK/MAPK targets / Regulation of MITF-M-dependent genes involved in pigmentation / fatty acid oxidation / MAP kinase kinase activity / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / signal transduction in response to DNA damage / JUN kinase activity / mitogen-activated protein kinase / chondrocyte differentiation / negative regulation of hippo signaling / positive regulation of myoblast differentiation / vascular endothelial growth factor receptor signaling pathway / skeletal muscle tissue development / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / cellular response to ionizing radiation / positive regulation of D-glucose import / activated TAK1 mediates p38 MAPK activation / stem cell differentiation / response to insulin / placenta development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of canonical Wnt signaling pathway / NOD1/2 Signaling Pathway / cell morphogenesis / bone development / cellular response to virus / platelet activation / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / glucose metabolic process / spindle pole / chemotaxis / positive regulation of reactive oxygen species metabolic process / osteoblast differentiation / cellular senescence / ADP signalling through P2Y purinoceptor 1 / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / secretory granule lumen / Oxidative Stress Induced Senescence / angiogenesis / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / transcription by RNA polymerase II / cell surface receptor signaling pathway / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / glutamatergic synapse / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm
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 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-HYW / Chem-I46 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBrown, D.G. / Hurley, C. / Irving, S.L.
CitationJournal: To Be Published
Title: P38 alpha complex with AR117045 and AR117046
Authors: Brown, D.G. / Irving, S.L.
History
DepositionJan 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,3223
Polymers41,4871
Non-polymers8352
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.880, 77.320, 65.350
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 Mitogen-activated protein kinase 14 / MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSBP / MAP kinase MXI2 / ...MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSBP / MAP kinase MXI2 / MAX-interacting protein 2 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / Stress-activated protein kinase 2a / SAPK2a


Mass: 41487.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG
References: UniProt: Q16539, mitogen-activated protein kinase
#2: Chemical ChemComp-I46 / 2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine


Mass: 257.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9F2N3
#3: Chemical ChemComp-HYW / 1-[5-~{tert}-butyl-2-(4-methylphenyl)pyrazol-3-yl]-3-[(1~{S},4~{R})-4-[(3-propan-2-yl-[1,2,4]triazolo[4,3-a]pyridin-6-yl)oxy]-1,2,3,4-tetrahydronaphthalen-1-yl]urea


Mass: 577.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H39N7O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 3000, Calcium Chloride, CHES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.85→53.47 Å / Num. obs: 32109 / % possible obs: 99.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.032 / Rrim(I) all: 0.069 / Net I/σ(I): 15.4
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.547 / Num. unique obs: 2352 / Rpim(I) all: 0.321 / Rrim(I) all: 0.697 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→53.47 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.284 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22154 1623 5.1 %RANDOM
Rwork0.1793 ---
obs0.18141 30448 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å20 Å2
2--1.33 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: 1 / Resolution: 1.85→53.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 62 154 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132783
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172604
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.643782
X-RAY DIFFRACTIONr_angle_other_deg1.4611.5756023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65922.027148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07915475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8951518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8012.1471308
X-RAY DIFFRACTIONr_mcbond_other1.7992.1441307
X-RAY DIFFRACTIONr_mcangle_it2.7673.1941629
X-RAY DIFFRACTIONr_mcangle_other2.7663.1971629
X-RAY DIFFRACTIONr_scbond_it2.2672.4131475
X-RAY DIFFRACTIONr_scbond_other2.2662.4131476
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6093.5152154
X-RAY DIFFRACTIONr_long_range_B_refined5.18725.2213177
X-RAY DIFFRACTIONr_long_range_B_other5.15825.1293164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 133 -
Rwork0.233 2216 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: -3.0133 Å / Origin y: 15.3222 Å / Origin z: -6.9172 Å
111213212223313233
T0.0264 Å2-0.0197 Å20.0041 Å2-0.0179 Å20.0012 Å2--0.0324 Å2
L0.6985 °20.1012 °20.0197 °2-0.2524 °20.0637 °2--1.1618 °2
S0.0011 Å °-0.0235 Å °0.0292 Å °0.0048 Å °-0.0272 Å °0.0001 Å °-0.1166 Å °0.0897 Å °0.0261 Å °

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