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- PDB-11oy: Crystal structure of Human p38 alpha MAPK in Complex with MW01-18... -

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Basic information

Entry
Database: PDB / ID: 11oy
TitleCrystal structure of Human p38 alpha MAPK in Complex with MW01-18-122SRM
ComponentsMitogen-activated protein kinase 14
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / PROTEIN KINASE DOMAIN / ATP BINDING / PHOSPHORYLATION / CYTOSOL
Function / homology
Function and homology information


positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / stress-induced premature senescence / stress-activated protein kinase signaling cascade / 3'-UTR-mediated mRNA stabilization / CD163 mediating an anti-inflammatory response / cell surface receptor protein serine/threonine kinase signaling pathway / positive regulation of myoblast fusion / KSRP (KHSRP) binds and destabilizes mRNA ...positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / stress-induced premature senescence / stress-activated protein kinase signaling cascade / 3'-UTR-mediated mRNA stabilization / CD163 mediating an anti-inflammatory response / cell surface receptor protein serine/threonine kinase signaling pathway / positive regulation of myoblast fusion / KSRP (KHSRP) binds and destabilizes mRNA / : / cellular response to UV-B / cartilage condensation / mitogen-activated protein kinase p38 binding / positive regulation of muscle cell differentiation / Myogenesis / Platelet sensitization by LDL / NFAT protein binding / positive regulation of myotube differentiation / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / p38MAPK cascade / ERK/MAPK targets / cellular response to lipoteichoic acid / response to dietary excess / fatty acid oxidation / response to muramyl dipeptide / MAP kinase kinase activity / Regulation of MITF-M-dependent genes involved in pigmentation / cellular response to vascular endothelial growth factor stimulus / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / RHO GTPases Activate NADPH Oxidases / vascular endothelial growth factor receptor signaling pathway / chondrocyte differentiation / negative regulation of hippo signaling / positive regulation of myoblast differentiation / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / skeletal muscle tissue development / positive regulation of brown fat cell differentiation / p38MAPK events / response to muscle stretch / signal transduction in response to DNA damage / striated muscle cell differentiation / positive regulation of interleukin-12 production / positive regulation of erythrocyte differentiation / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / DNA damage checkpoint signaling / placenta development / stem cell differentiation / tumor necrosis factor-mediated signaling pathway / positive regulation of D-glucose import across plasma membrane / cellular response to ionizing radiation / activated TAK1 mediates p38 MAPK activation / negative regulation of inflammatory response to antigenic stimulus / negative regulation of canonical Wnt signaling pathway / NOD1/2 Signaling Pathway / platelet activation / cellular response to virus / response to insulin / positive regulation of protein import into nucleus / bone development / VEGFA-VEGFR2 Pathway / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / cell morphogenesis / chemotaxis / spindle pole / osteoblast differentiation / cellular senescence / ADP signalling through P2Y purinoceptor 1 / MAPK cascade / cellular response to lipopolysaccharide / angiogenesis / secretory granule lumen / protein phosphatase binding / Oxidative Stress Induced Senescence / transcription by RNA polymerase II / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / nuclear speck / intracellular signal transduction / 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 / 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
: / 4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.022 Å
AuthorsBrunzelle, J.S. / Shuvalova, L. / Roy, S.M. / Watterson, D.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)NIH AG031311 NIH AG043415 United States
CitationJournal: To Be Published
Title: Crystal structure of Human p38 alpha MAPK in Complex with MW01-18-122SRM
Authors: Brunzelle, J.S. / Shuvalova, L. / Roy, S.M. / Watterson, D.M.
History
DepositionMar 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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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)42,0294
Polymers41,3431
Non-polymers6863
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.760, 74.507, 78.975
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 / MAP kinase 14 / MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSAID- ...MAP kinase 14 / MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSAID-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: 41343.195 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 (E. coli)
References: UniProt: Q16539, mitogen-activated protein kinase
#2: Chemical ChemComp-GG5 / 4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE


Mass: 239.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10FN3
#3: Chemical ChemComp-A1C99 / (3P)-6-(4-methylpiperazin-1-yl)-3-(naphthalen-1-yl)-4-(pyridin-4-yl)pyridazine


Mass: 381.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 10000 0.1M Ammonium Acetate 0.1M Bis-Tris (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 20, 2025 / Details: Be lens
RadiationMonochromator: Diamond Laue 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.02→54.2 Å / Num. obs: 26450 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 49.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.016 / Rrim(I) all: 0.058 / Χ2: 0.71 / Net I/σ(I): 19.9 / Num. measured all: 359469
Reflection shellResolution: 2.02→2.13 Å / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 1.118 / Num. measured all: 53326 / Num. unique obs: 3805 / CC1/2: 0.882 / Rpim(I) all: 0.308 / Rrim(I) all: 1.16 / Χ2: 0.53 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (17-JUL-2025)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
autoPROCdata processing
DIMPLEphasing
RefinementMethod to determine structure: SIR / Resolution: 2.022→54.2 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.157
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1244 4.71 %RANDOM
Rwork0.2109 ---
obs0.212 26398 100 %-
Displacement parametersBiso mean: 61.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.0583 Å20 Å20 Å2
2--5.9854 Å20 Å2
3----7.0438 Å2
Refine analyzeLuzzati coordinate error obs: 0.271 Å
Refinement stepCycle: LAST / Resolution: 2.022→54.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 48 142 2911
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082843HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.893863HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d985SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes487HARMONIC5
X-RAY DIFFRACTIONt_it2843HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion16.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion363SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2305SEMIHARMONIC4
LS refinement shellResolution: 2.022→2.04 Å
RfactorNum. reflection% reflection
Rfree0.4322 -3.98 %
Rwork0.2844 507 -
obs--98.17 %
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)
116.88462.96342.020217.7935-1.43859.2563-0.0146-0.5908-0.01880.47840.64271.4665-0.4949-0.641-0.628-0.3171-0.03260.1655-0.13510.25520.0576-16.0252-0.156621.5936
25.0264-1.1278-0.72135.6081-2.75783.93480.3211-0.0174-0.10470.12740.13710.5522-0.2222-0.307-0.4581-0.214-0.02290.0242-0.24640.0291-0.1119-5.34644.02114.8499
35.44480.3760.4745.6684-0.47453.94420.1059-0.0626-0.32710.0584-0.14740.11110.238-0.10770.0415-0.1472-0.00210.0063-0.23910.0285-0.12539.8819-3.351817.2752
45.04551.4731-0.0113.76970.06563.079-0.0074-0.0440.70210.1155-0.01320.0483-0.25570.06590.0206-0.15190.0026-0.0247-0.18520.047-0.000222.2213.010118.3319
54.2513-0.71731.01363.5175-0.3411.85680.11420.0755-0.39510.077-0.1017-0.61480.07480.304-0.0125-0.18110.02530.0211-0.20880.0616-0.130923.4559-2.197615.8316
611.33331.9647-3.374118.6841-7.762311.44540.23941.04440.5592-0.66170.45521.50990.4681-0.82-0.6945-0.18590.072-0.1305-0.11870.0797-0.3683-7.89378.3412.5343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|5 - A|49 }
2X-RAY DIFFRACTION2{ A|50 - A|122 }
3X-RAY DIFFRACTION3{ A|123 - A|169 }
4X-RAY DIFFRACTION4{ A|170 - A|261 }
5X-RAY DIFFRACTION5{ A|262 - A|324 }
6X-RAY DIFFRACTION6{ A|325 - A|353 }

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