+Open data
-Basic information
Entry | Database: PDB / ID: 6sk9 | |||||||||
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Title | Nek2 bound to purine compound 51 | |||||||||
Components | Serine/threonine-protein kinase Nek2 | |||||||||
Keywords | TRANSFERASE / Ser/Thr protein kinase | |||||||||
Function / homology | Function and homology information negative regulation of centriole-centriole cohesion / centrosome separation / regulation of attachment of spindle microtubules to kinetochore / regulation of mitotic centrosome separation / regulation of mitotic nuclear division / positive regulation of telomere capping / blastocyst development / mitotic spindle assembly / spindle assembly / Loss of Nlp from mitotic centrosomes ...negative regulation of centriole-centriole cohesion / centrosome separation / regulation of attachment of spindle microtubules to kinetochore / regulation of mitotic centrosome separation / regulation of mitotic nuclear division / positive regulation of telomere capping / blastocyst development / mitotic spindle assembly / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of telomerase activity / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of telomere maintenance via telomerase / APC-Cdc20 mediated degradation of Nek2A / AURKA Activation by TPX2 / meiotic cell cycle / condensed nuclear chromosome / chromosome segregation / kinetochore / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / midbody / protein phosphatase binding / microtubule / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / protein-containing complex / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Bayliss, R. / Byrne, M.J. / Mas-Droux, C. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Biochem.J. / Year: 2020 Title: Nek7 conformational flexibility and inhibitor binding probed through protein engineering of the R-spine. Authors: Byrne, M.J. / Nasir, N. / Basmadjian, C. / Bhatia, C. / Cunnison, R.F. / Carr, K.H. / Mas-Droux, C. / Yeoh, S. / Cano, C. / Bayliss, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sk9.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sk9.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/6sk9 ftp://data.pdbj.org/pub/pdb/validation_reports/sk/6sk9 | HTTPS FTP |
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-Related 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: 32662.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEK2, NEK2A, NLK1 / Production host: Escherichia coli (E. coli) References: UniProt: P51955, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-F9N / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.33 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop Details: 50 mM Hepes, pH 7.5, 300 mM sodium chloride, 10 mM sodium phosphate, 5 mM dithiothreitol and 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→30.63 Å / Num. obs: 21992 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.3770207207 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2→2.11 Å / Num. unique obs: 3167 / CC1/2: 0.679 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.63 Å / SU ML: 0.186498588615 / Cross valid method: FREE R-VALUE / σ(F): 1.35040804944 / Phase error: 23.177789498
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.6367037345 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30.63 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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