+Open data
-Basic information
Entry | Database: PDB / ID: 3npc | ||||||
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Title | Crystal structure of JNK2 complexed with BIRB796 | ||||||
Components | Mitogen-activated protein kinase 9 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / DFG-out / Protein kinase / Transferase / ATP Binding / type II kinase inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information protein localization to tricellular tight junction / JUN kinase activity / inflammatory response to wounding / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / JNK cascade ...protein localization to tricellular tight junction / JUN kinase activity / inflammatory response to wounding / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / JNK cascade / cellular response to cadmium ion / protein serine/threonine/tyrosine kinase activity / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of protein ubiquitination / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / FCERI mediated MAPK activation / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / regulation of circadian rhythm / cellular response to reactive oxygen species / cellular senescence / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å | ||||||
Authors | Kuglstatter, A. / Ghate, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: X-ray crystal structure of JNK2 complexed with the p38alpha inhibitor BIRB796: Insights into the rational design of DFG-out binding MAP kinase inhibitors. Authors: Kuglstatter, A. / Ghate, M. / Tsing, S. / Villasenor, A.G. / Shaw, D. / Barnett, J.W. / Browner, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3npc.cif.gz | 159.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3npc.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 3npc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/3npc ftp://data.pdbj.org/pub/pdb/validation_reports/np/3npc | HTTPS FTP |
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-Related structure data
Related structure data | 3e7oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 41896.328 Da / Num. of mol.: 2 / Fragment: UNP residues 1-364 / Mutation: D3K, C6V, S8N, Q14E, K203A, E204A, K250A, K251A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK9, JNK2, PRKM9 / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P45984, mitogen-activated protein kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 0.1M sodium chloride, 1.6M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 33595 / % possible obs: 99.9 % / Biso Wilson estimate: 34.6 Å2 / Rsym value: 0.084 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.35→2.43 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.569 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3E7O Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.99 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.521 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.351→2.412 Å / Total num. of bins used: 20
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