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Open data
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Basic information
Entry | Database: PDB / ID: 5n7v | ||||||
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Title | TTK kinase domain in complex with MPI-0479605 | ||||||
![]() | Dual specificity protein kinase TTK | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Uitdehaag, J. / Willemsen-Seegers, N. / 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 | ![]() | 74.1 KB | Display | ![]() |
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PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5n84C ![]() 5n87C ![]() 5n93C ![]() 5n9sC ![]() 5na0C ![]() 5nadC ![]() 3cekS S: Starting model for refinement C: citing same article ( |
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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-8PT / ~{ | ||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.82 % |
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Crystal grow![]() | Temperature: 273 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.52→41.33 Å / Num. obs: 15719 / % possible obs: 99.9 % / Redundancy: 6.48 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.52→2.62 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1740 / CC1/2: 0.783 / Rpim(I) all: 0.435 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3CEK Resolution: 2.52→41.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.962 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.279 / 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: 88.663 Å2
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Refinement step | Cycle: 1 / Resolution: 2.52→41.33 Å
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Refine LS restraints |
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