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Yorodumi- PDB-4o6l: Crystal Structure of TTK kinase domain with an inhibitor: 401498 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o6l | ||||||
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Title | Crystal Structure of TTK kinase domain with an inhibitor: 401498 (N-[(1R)-1-(2-chlorophenyl)propyl]-3-{4-[(1-methylpiperidin-4-yl)oxy]phenyl}-1H-indazole-5-carboxamide) | ||||||
Components | Dual specificity protein kinase TTK | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / TTK / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / spindle / kinetochore / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / membrane / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Qiu, W. / Plotnikova, O. / Feher, M. / Awrey, D.E. / Chirgadze, N.Y. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of TTK kinase domain with an inhibitor: 401498 Authors: Qiu, W. / Plotnikova, O. / Feher, M. / Awrey, D.E. / Chirgadze, N.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o6l.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o6l.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 4o6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/4o6l ftp://data.pdbj.org/pub/pdb/validation_reports/o6/4o6l | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32699.236 Da / Num. of mol.: 2 / Fragment: kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1, MPS1L1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33981, dual-specificity kinase #2: Chemical | #3: Chemical | #4: 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: 3.21 Å3/Da / Density % sol: 61.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.2M Ammonium Sulfate, 0.1M HEPES pH7.5, 25% PEG3350, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→100 Å / Num. all: 33447 / Num. obs: 33229 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.66 % / Biso Wilson estimate: 54.97 Å2 / Rmerge(I) obs: 0.0656 / Rsym value: 0.037 / Net I/σ(I): 14.47 |
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 6.61 % / Rmerge(I) obs: 0.5077 / Mean I/σ(I) obs: 2.03 / Num. unique all: 3484 / Rsym value: 0.4769 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→38.269 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 33.03 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→38.269 Å
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Refine LS restraints |
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LS refinement shell |
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