+Open data
-Basic information
Entry | Database: PDB / ID: 6s76 | |||||||||
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Title | Crystal structure of human Nek7 | |||||||||
Components | Serine/threonine-protein kinase Nek7 | |||||||||
Keywords | CELL CYCLE / Kinase | |||||||||
Function / homology | Function and homology information NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / cellular response to potassium ion / Nuclear Pore Complex (NPC) Disassembly / microtubule organizing center / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of telomere capping / spindle assembly / EML4 and NUDC in mitotic spindle formation / positive regulation of telomerase activity ...NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / cellular response to potassium ion / Nuclear Pore Complex (NPC) Disassembly / microtubule organizing center / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of telomere capping / spindle assembly / EML4 and NUDC in mitotic spindle formation / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / regulation of mitotic cell cycle / molecular function activator activity / spindle pole / microtubule / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å | |||||||||
Authors | Nasir, N. / Bayliss, R. | |||||||||
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 | 6s76.cif.gz | 414 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s76.ent.gz | 273 KB | Display | PDB format |
PDBx/mmJSON format | 6s76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/6s76 ftp://data.pdbj.org/pub/pdb/validation_reports/s7/6s76 | HTTPS FTP |
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-Related structure data
Related structure data | 6s73C 6s75C 6sk9C 6gt1 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 35670.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEK7 / Production host: Escherichia coli (E. coli) References: UniProt: Q8TDX7, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-PEG / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3.38→74.74 Å / Num. obs: 19383 / % possible obs: 99.46 % / Redundancy: 3.3 % / Biso Wilson estimate: 88.34 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.101 / Net I/σ(I): 6.54 |
Reflection shell | Resolution: 3.38→3.5 Å / Num. unique obs: 6623 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GT1 6gt1 Resolution: 3.38→74.74 Å / SU ML: 0.4454 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.5528
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.38→74.74 Å
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Refine LS restraints |
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LS refinement shell |
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