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- PDB-7bdq: MAPK14 bound with SR300 -

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Basic information

Entry
Database: PDB / ID: 7bdq
TitleMAPK14 bound with SR300
ComponentsMitogen-activated protein kinase 14
KeywordsTRANSFERASE / p38a / Inhibitor / MAPK14 / Structural Genomics / Structural Genomics Consortium / SGC
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 / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / Regulation of MITF-M-dependent genes involved in pigmentation / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence ...p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / Regulation of MITF-M-dependent genes involved in pigmentation / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / ADP signalling through P2Y purinoceptor 1 / 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 / positive regulation of myoblast fusion / cellular response to UV-B / cartilage condensation / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / D-glucose import / p38MAPK cascade / fatty acid oxidation / response to dietary excess / cellular response to lipoteichoic acid / response to muramyl dipeptide / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / negative regulation of hippo signaling / positive regulation of myoblast differentiation / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / response to muscle stretch / striated muscle cell differentiation / Neutrophil degranulation / positive regulation of interleukin-12 production / positive regulation of erythrocyte differentiation / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / DNA damage checkpoint signaling / placenta development / tumor necrosis factor-mediated signaling pathway / positive regulation of D-glucose import / cellular response to ionizing radiation / stem cell differentiation / negative regulation of canonical Wnt signaling pathway / response to insulin / bone development / cellular response to virus / positive regulation of protein import into nucleus / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / cell morphogenesis / spindle pole / osteoblast differentiation / cellular response to tumor necrosis factor / kinase activity / MAPK cascade / cellular response to lipopolysaccharide / angiogenesis / protein phosphatase binding / 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 / apoptotic process / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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-TJZ / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSchroeder, M. / Roehm, S. / Joerger, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2021
Title: Development of a Selective Dual Discoidin Domain Receptor (DDR)/p38 Kinase Chemical Probe.
Authors: Rohm, S. / Berger, B.T. / Schroder, M. / Chatterjee, D. / Mathea, S. / Joerger, A.C. / Pinkas, D.M. / Bufton, J.C. / Tjaden, A. / Kovooru, L. / Kudolo, M. / Pohl, C. / Bullock, A.N. / ...Authors: Rohm, S. / Berger, B.T. / Schroder, M. / Chatterjee, D. / Mathea, S. / Joerger, A.C. / Pinkas, D.M. / Bufton, J.C. / Tjaden, A. / Kovooru, L. / Kudolo, M. / Pohl, C. / Bullock, A.N. / Muller, S. / Laufer, S. / Knapp, S.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,3875
Polymers41,3951
Non-polymers9924
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint14 kcal/mol
Surface area15980 Å2
Unit cell
Length a, b, c (Å)65.027, 73.041, 74.347
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 / MAPK 14 / CRK1 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha


Mass: 41395.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli (E. coli)
References: UniProt: P47811, mitogen-activated protein kinase
#2: Chemical ChemComp-TJZ / ~{N}-[(2~{S})-4-cyclohexyl-1-[[(3~{R})-1-methylsulfonylpiperidin-3-yl]amino]-1-oxidanylidene-butan-2-yl]-4-[[(1-phenylpyrazolo[3,4-d]pyrimidin-4-yl)amino]methyl]benzamide


Mass: 672.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H44N8O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 14% HMW PgSmear, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→48.95 Å / Num. obs: 9622 / % possible obs: 99.6 % / Redundancy: 4.4 % / CC1/2: 0.977 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.11 / Rrim(I) all: 0.244 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.75-2.94.61.544628413760.4460.7741.7352.799.7
8.7-48.953.90.09114143610.9870.0470.1038.899.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
Aimless0.7.4data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lar

5lar


Resolution: 2.75→48.9 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 36.044 / SU ML: 0.35 / SU R Cruickshank DPI: 0.3594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 461 4.8 %RANDOM
Rwork0.2155 ---
obs0.2178 9124 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110 Å2 / Biso mean: 47.177 Å2 / Biso min: 19.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å2-0 Å2
2---0.49 Å20 Å2
3----0.91 Å2
Refinement stepCycle: final / Resolution: 2.75→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2596 0 68 28 2692
Biso mean--56.81 43.93 -
Num. residues----336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132730
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172525
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.6333725
X-RAY DIFFRACTIONr_angle_other_deg1.191.65781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9865334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6522.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50115407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4891514
X-RAY DIFFRACTIONr_chiral_restr0.0550.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02622
LS refinement shellResolution: 2.75→2.822 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 27 -
Rwork0.311 674 -
all-701 -
obs--99.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8552-1.1173-1.69993.54382.53994.450.20620.0620.6962-0.3238-0.03950.2956-0.5245-0.4733-0.16670.06650.00990.01310.50040.06770.21734.48933.19519.681
25.36811.44890.6822.12770.64312.9289-0.115-0.21670.42370.0689-0.00110.2217-0.1553-0.02270.11610.01980.0298-0.00390.34970.0030.041320.21832.37723.671
33.99882.54053.32941.78210.686715.1675-0.62150.79590.3217-0.51640.54170.25920.59930.52480.07980.2467-0.05450.02110.52510.05160.440832.70832.8167.298
42.62750.12721.20131.23140.76662.9066-0.04130.0723-0.0918-0.12560.1078-0.4725-0.2030.5878-0.06650.02610.00970.02350.5202-0.06490.231939.7733.25215.422
54.5061-0.4153-2.40444.7326-0.502411.2482-0.22290.1164-0.2282-0.09070.06150.32960.5222-0.41490.16140.1575-0.0255-0.0820.3214-0.03480.14566.97719.50712.388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 78
2X-RAY DIFFRACTION2A79 - 185
3X-RAY DIFFRACTION3A186 - 202
4X-RAY DIFFRACTION4A203 - 324
5X-RAY DIFFRACTION5A325 - 353

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