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- PDB-5na0: TTK kinase domain in complex with a PEG-linked pyrimido-indolizine -
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Open data
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Basic information
Entry | Database: PDB / ID: 5na0 | ||||||
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Title | TTK kinase domain in complex with a PEG-linked pyrimido-indolizine | ||||||
![]() | Dual specificity protein kinase TTK | ||||||
![]() | TRANSFERASE / kinase / inhibitor / mitosis / Mps1 | ||||||
Function / homology | ![]() 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 / phosphorylation / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Uitdehaag, J. / Willemsen-Seegers, N. / de Man, J. / Buijsman, R.C. / Zaman, G.J.R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.2 KB | Display | ![]() |
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PDB format | ![]() | 49.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 719 KB | Display | ![]() |
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Full document | ![]() | 726.3 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n7vSC ![]() 5n84C ![]() 5n87C ![]() 5n93C ![]() 5n9sC ![]() 5nadC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36211.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-8QZ / ~{ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.8 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 24, 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: 2.9→80.98 Å / Num. obs: 10632 / % possible obs: 99.5 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.066 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.085 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1662 / CC1/2: 0.647 / Rpim(I) all: 0.642 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N7V Resolution: 2.9→60.59 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 16.223 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.907 / ESU R Free: 0.386 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.95 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→60.59 Å
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Refine LS restraints |
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