+Open data
-Basic information
Entry | Database: PDB / ID: 5nad | ||||||
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Title | TTK kinase domain in complex with BAY 1217389 | ||||||
Components | Dual specificity protein kinase TTK | ||||||
Keywords | TRANSFERASE / kinase / inhibitor / mitosis / Mps1 | ||||||
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 / kinetochore / spindle / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Uitdehaag, J.C.M. / Willemsen-Seegers, N. / Sterrenburg, J.G. / de Man, J. / Buijsman, R.C. / Zaman, G.J.R. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2017 Title: Target Residence Time-Guided Optimization on TTK Kinase Results in Inhibitors with Potent Anti-Proliferative Activity. Authors: Uitdehaag, J.C.M. / de Man, J. / Willemsen-Seegers, N. / Prinsen, M.B.W. / Libouban, M.A.A. / Sterrenburg, J.G. / de Wit, J.J.P. / de Vetter, J.R.F. / de Roos, J.A.D.M. / Buijsman, R.C. / Zaman, G.J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nad.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nad.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 5nad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/5nad ftp://data.pdbj.org/pub/pdb/validation_reports/na/5nad | HTTPS FTP |
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-Related structure data
Related structure data | 5n7vSC 5n84C 5n87C 5n93C 5n9sC 5na0C S: Starting model for refinement C: citing same article (ref.) |
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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: 36211.277 Da / Num. of mol.: 1 / Fragment: UNP residues 519-808 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 |
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#2: Chemical | ChemComp-8RH / |
#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: 3.05 Å3/Da / Density % sol: 59.7 % / Description: clear prism shape |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 32 - 37% PEG400 (Acros, Geel, Belgium), 0.1 M Na/K phosphate pH 6.3 and 250 mM NaCl.pH 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→79.19 Å / Num. obs: 11158 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.057 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.8→2.99 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1972 / CC1/2: 0.611 / Rpim(I) all: 0.562 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N7V Resolution: 2.8→79.19 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / SU B: 15.578 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.632 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.214 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→79.19 Å
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Refine LS restraints |
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