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Yorodumi- PDB-2zdt: Crystal Structure of human JNK3 complexed with an isoquinolone in... -
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-Basic information
Entry | Database: PDB / ID: 2zdt | ||||||
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Title | Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor | ||||||
Components | Mitogen-activated protein kinase 10 | ||||||
Keywords | TRANSFERASE / PROTEIN KINASE / ATP-binding / Epilepsy / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm ...JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm / rhythmic process / cellular senescence / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sogabe, S. / Asano, Y. / Fukumoto, S. / Habuka, N. / Fujishima, A. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2008 Title: Discovery, synthesis and biological evaluation of isoquinolones as novel and highly selective JNK inhibitors (2) Authors: Asano, Y. / Kitamura, S. / Ohra, T. / Itoh, F. / Kajino, M. / Tamura, T. / Kaneko, M. / Ikeda, S. / Igata, H. / Kawamoto, T. / Sogabe, S. / Matsumoto, S. / Tanaka, T. / Yamaguchi, M. / Kimura, H. / Fukumoto, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zdt.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zdt.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/2zdt ftp://data.pdbj.org/pub/pdb/validation_reports/zd/2zdt | HTTPS FTP |
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-Related structure data
Related structure data | 1jnkS 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: 42059.676 Da / Num. of mol.: 1 / Fragment: Residues UNP 39-402 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21alpha / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P53779, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-46C / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 46.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% Pentaerythritol ethoxylate (15/4 EO/OH), 0.1M ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 26941 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.61 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.27 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 4.8 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JNK Resolution: 2→45.63 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1625443.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.9264 Å2 / ksol: 0.381535 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→45.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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