+Open data
-Basic information
Entry | Database: PDB / ID: 4eyj | ||||||
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Title | MAPK13 Complex with inhibitor | ||||||
Components | Mitogen-activated protein kinase 13 | ||||||
Keywords | Transferase/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 / cellular response to interleukin-1 / MAP kinase activity / mitogen-activated protein kinase / stress-activated MAPK cascade / p38MAPK events / NOD1/2 Signaling Pathway ...cellular response to anisomycin / cellular response to sorbitol / cellular response to sodium arsenite / response to osmotic stress / cellular response to interleukin-1 / MAP kinase activity / mitogen-activated protein kinase / stress-activated MAPK cascade / p38MAPK events / NOD1/2 Signaling Pathway / VEGFA-VEGFR2 Pathway / positive regulation of interleukin-6 production / cellular response to hydrogen peroxide / positive regulation of inflammatory response / cellular response to UV / peptidyl-serine phosphorylation / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.102 Å | ||||||
Authors | Miller, C.A. / Brett, T.J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eyj.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eyj.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 4eyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4eyj_validation.pdf.gz | 689 KB | Display | wwPDB validaton report |
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Full document | 4eyj_full_validation.pdf.gz | 693.2 KB | Display | |
Data in XML | 4eyj_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4eyj_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/4eyj ftp://data.pdbj.org/pub/pdb/validation_reports/ey/4eyj | HTTPS FTP |
-Related structure data
Related structure data | 4eymC 4ynoC 4exu C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-N61 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 25, 2011 / Details: double crystal |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 4EXU 4exu Resolution: 2.102→36.9 Å / SU ML: 0.59 / σ(F): 1.33 / Phase error: 31.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage 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 |
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Refinement step | Cycle: LAST / Resolution: 2.102→36.9 Å
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Refine LS restraints |
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LS refinement shell |
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