+Open data
-Basic information
Entry | Database: PDB / ID: 6tnb | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY STRUCTURE OF MPS1 IN COMPLEX WITH COMPOUND 41 | ||||||
Components | Dual specificity protein kinase TTK | ||||||
Keywords | CELL CYCLE / Kinase / 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 / 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: 2.65 Å | ||||||
Authors | Holton, S.J. / Schulze, V.K. / Klar, U. / Kosemund, D. / Siemeister, G. / Bader, B. / Prechtl, S. / Briem, H. / Marquardt, T. / Schirok, H. ...Holton, S.J. / Schulze, V.K. / Klar, U. / Kosemund, D. / Siemeister, G. / Bader, B. / Prechtl, S. / Briem, H. / Marquardt, T. / Schirok, H. / Bohlmann, R. / Nguyen, D. / Fernandez-Montalvan, A. / Boemer, U. / Eberspaecher, U. / Brands, M. / Nussbaum, F. / Koppitz, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Treating Cancer by Spindle Assembly Checkpoint Abrogation: Discovery of Two Clinical Candidates, BAY 1161909 and BAY 1217389, Targeting MPS1 Kinase. Authors: Schulze, V.K. / Klar, U. / Kosemund, D. / Wengner, A.M. / Siemeister, G. / Stockigt, D. / Neuhaus, R. / Lienau, P. / Bader, B. / Prechtl, S. / Holton, S.J. / Briem, H. / Marquardt, T. / ...Authors: Schulze, V.K. / Klar, U. / Kosemund, D. / Wengner, A.M. / Siemeister, G. / Stockigt, D. / Neuhaus, R. / Lienau, P. / Bader, B. / Prechtl, S. / Holton, S.J. / Briem, H. / Marquardt, T. / Schirok, H. / Jautelat, R. / Bohlmann, R. / Nguyen, D. / Fernandez-Montalvan, A.E. / Bomer, U. / Eberspaecher, U. / Bruning, M. / Dohr, O. / Raschke, M. / Kreft, B. / Mumberg, D. / Ziegelbauer, K. / Brands, M. / von Nussbaum, F. / Koppitz, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tnb.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tnb.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/6tnb ftp://data.pdbj.org/pub/pdb/validation_reports/tn/6tnb | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33850.738 Da / Num. of mol.: 1 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 | ChemComp-8QW / ( |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.23 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.54 Details: 1.2M Ammonium sulphate, 100mM sodium cacodylate pH 6.54m 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→77.23 Å / Num. obs: 12008 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.65→2.83 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 1404 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: unpublished Resolution: 2.65→35.15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 16.015 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.447 / ESU R Free: 0.298 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.71 Å2 / Biso mean: 80.611 Å2 / Biso min: 30.21 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→35.15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.65→2.717 Å / Rfactor Rfree error: 0
|