[English] 日本語
Yorodumi- PDB-2waj: Crystal structure of human Jnk3 complexed with a 1-aryl-3,4- dihy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2waj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human Jnk3 complexed with a 1-aryl-3,4- dihydroisoquinoline inhibitor | ||||||
Components | MITOGEN-ACTIVATED PROTEIN KINASE 10 | ||||||
Keywords | TRANSFERASE / KINASE / EPILEPSY / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / PHOSPHOPROTEIN / PROTEIN KINASE / NUCLEOTIDE-BINDING | ||||||
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 / regulation of circadian rhythm / FCERI mediated MAPK activation ...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 / regulation of circadian rhythm / FCERI mediated MAPK activation / cellular senescence / rhythmic process / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Bax, B.D. / Christopher, J.A. / Jones, E.J. / Mosley, J.E. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: 1-Aryl-3,4-Dihydroisoquinoline Inhibitors of Jnk3. Authors: Christopher, J.A. / Atkinson, F.L. / Bax, B.D. / Brown, M.J. / Champigny, A.C. / Chuang, T.T. / Jones, E.J. / Mosley, J.E. / Musgrave, J.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2waj.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2waj.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 2waj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/2waj ftp://data.pdbj.org/pub/pdb/validation_reports/wa/2waj | HTTPS FTP |
---|
-Related structure data
Related structure data | 2o0uS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42059.676 Da / Num. of mol.: 1 / Fragment: RESIDUES, 39-402 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P53779, mitogen-activated protein kinase |
---|---|
#2: Chemical | ChemComp-SNB / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
---|---|
Crystal grow | Details: 18% PEG3350, 0.1M SODIUM HEPES PH7.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→22.71 Å / Num. obs: 15942 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O0U Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.897 / SU B: 18.721 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.472 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|