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- PDB-4eyj: MAPK13 Complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4eyj
TitleMAPK13 Complex with inhibitor
ComponentsMitogen-activated protein kinase 13P38 mitogen-activated protein kinases
KeywordsTransferase/Transferase Inhibitor / p38 family kinase / map kinase / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


cellular response to anisomycin / cellular response to sorbitol / cellular response to sodium arsenite / response to osmotic stress / DSCAM interactions / MAP kinase activity / mitogen-activated protein kinase / cellular response to interleukin-1 / stress-activated MAPK cascade / p38MAPK events ...cellular response to anisomycin / cellular response to sorbitol / cellular response to sodium arsenite / response to osmotic stress / DSCAM interactions / MAP kinase activity / mitogen-activated protein kinase / cellular response to interleukin-1 / stress-activated MAPK cascade / p38MAPK events / NOD1/2 Signaling Pathway / cellular response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to UV / peptidyl-serine phosphorylation / intracellular signal transduction / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase 13 / 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 ...Mitogen-activated protein kinase 13 / 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-N61 / Mitogen-activated protein kinase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.102 Å
AuthorsMiller, C.A. / Brett, T.J.
CitationJournal: J.Clin.Invest. / Year: 2012
Title: IL-13-induced airway mucus production is attenuated by MAPK13 inhibition.
Authors: Alevy, Y.G. / Patel, A.C. / Romero, A.G. / Patel, D.A. / Tucker, J. / Roswit, W.T. / Miller, C.A. / Heier, R.F. / Byers, D.E. / Brett, T.J. / Holtzman, M.J.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9992
Polymers42,6341
Non-polymers3651
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.855, 69.955, 92.807
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 13 / P38 mitogen-activated protein kinases / MAP kinase 13 / MAPK 13 / Mitogen-activated protein kinase p38 delta / MAP kinase p38 delta / ...MAP kinase 13 / MAPK 13 / Mitogen-activated protein kinase p38 delta / MAP kinase p38 delta / Stress-activated protein kinase 4


Mass: 42633.898 Da / Num. of mol.: 1 / Fragment: UNP residues 1-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK13, PRKM13, SAPK4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: O15264, mitogen-activated protein kinase
#2: Chemical ChemComp-N61 / 1-(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)-3-[4-(pyridin-4-yloxy)phenyl]urea


Mass: 365.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM ammonium tartrate, 18% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 25, 2011 / Details: double crystal
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 21432 / Num. obs: 21432 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 26
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.36 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4EXU

4exu
PDB Unreleased entry


Resolution: 2.102→36.9 Å / SU ML: 0.59 / σ(F): 1.33 / Phase error: 31.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2749 1057 5.03 %
Rwork0.242 --
obs0.2437 21034 88.78 %
all-21034 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.122 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.7373 Å2-0 Å2-0 Å2
2---7.0264 Å20 Å2
3----6.7109 Å2
Refinement stepCycle: LAST / Resolution: 2.102→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 27 276 3052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042848
X-RAY DIFFRACTIONf_angle_d0.8443850
X-RAY DIFFRACTIONf_dihedral_angle_d15.8951077
X-RAY DIFFRACTIONf_chiral_restr0.066416
X-RAY DIFFRACTIONf_plane_restr0.003488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.102-2.19730.34331380.27652672X-RAY DIFFRACTION98
2.1973-2.31310.6859470.49561042X-RAY DIFFRACTION37
2.3131-2.4580.33421530.2852746X-RAY DIFFRACTION99
2.458-2.64780.30261340.25092786X-RAY DIFFRACTION99
2.6478-2.91410.26941490.25592796X-RAY DIFFRACTION100
2.9141-3.33560.28721530.24622795X-RAY DIFFRACTION100
3.3356-4.20150.29021080.22362191X-RAY DIFFRACTION77
4.2015-36.90540.19851750.2022949X-RAY DIFFRACTION99

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