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- PDB-6qdz: P38 alpha complex with AR117045 -

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Basic information

Entry
Database: PDB / ID: 6qdz
TitleP38 alpha complex with AR117045
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 / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation ...stress-activated protein kinase signaling cascade / positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation / positive regulation of myoblast fusion / cellular response to UV-B / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / positive regulation of muscle cell differentiation / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / D-glucose import / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / p38MAPK cascade / 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 / MAP kinase activity / RHO GTPases Activate NADPH Oxidases / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / signal transduction in response to DNA damage / mitogen-activated protein kinase / negative regulation of hippo signaling / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / 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 / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / positive regulation of D-glucose import / stem cell differentiation / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / negative regulation of inflammatory response to antigenic stimulus / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / placenta development / NOD1/2 Signaling Pathway / cellular response to virus / platelet activation / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / glucose metabolic process / ADP signalling through P2Y purinoceptor 1 / chemotaxis / positive regulation of reactive oxygen species metabolic process / cellular senescence / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / angiogenesis / secretory granule lumen / Oxidative Stress Induced Senescence / 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 / glutamatergic synapse / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / apoptotic process / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding
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. / : / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
Similarity search - Domain/homology
Chem-HYK / Chem-I46 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBrown, D.G. / Hurley, C. / Irving, S.L.
CitationJournal: To Be Published
Title: P38 alpha complex with AR117045
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 ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.351, 73.990, 77.671
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-HYK / 1-[5-~{tert}-butyl-2-(4-methylphenyl)pyrazol-3-yl]-3-[(1~{S},4~{S})-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.: 157 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
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: 1.73→27.9 Å / Num. obs: 39035 / % possible obs: 97.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.073 / Rrim(I) all: 0.099 / Net I/σ(I): 8.5
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 2.7 % / Rmerge(I) obs: 2.072 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2370 / Rpim(I) all: 1.378 / Rrim(I) all: 2.575 / % possible all: 82.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→27.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.613 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1947 5 %RANDOM
Rwork0.20346 ---
obs0.20559 36804 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å2-0 Å2
2---0.39 Å20 Å2
3---1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.73→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 62 157 2862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132776
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172587
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.6393775
X-RAY DIFFRACTIONr_angle_other_deg1.4231.5745986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9585325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99622.027148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36315471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3671518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2356
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_it1.9682.2731306
X-RAY DIFFRACTIONr_mcbond_other1.9692.2721305
X-RAY DIFFRACTIONr_mcangle_it2.9883.3841627
X-RAY DIFFRACTIONr_mcangle_other2.9883.3861627
X-RAY DIFFRACTIONr_scbond_it2.4262.5411470
X-RAY DIFFRACTIONr_scbond_other2.4252.5411471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8613.7082148
X-RAY DIFFRACTIONr_long_range_B_refined5.45726.6663143
X-RAY DIFFRACTIONr_long_range_B_other5.42426.5243123
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.727→1.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 93 -
Rwork0.379 2050 -
obs--73.67 %
Refinement TLS params.Method: refined / Origin x: -6.9053 Å / Origin y: -3.074 Å / Origin z: 15.2654 Å
111213212223313233
T0.0016 Å2-0.0011 Å20.0063 Å2-0.0502 Å2-0.0241 Å2--0.0812 Å2
L0.5505 °20.0041 °20.0568 °2-0.3029 °20.0615 °2--0.0502 °2
S0.0255 Å °-0.0598 Å °0.0452 Å °-0.0034 Å °-0.0082 Å °-0.0124 Å °0.0013 Å °-0.0079 Å °-0.0173 Å °

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