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Open data
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Basic information
Entry | Database: PDB / ID: 6s76 | |||||||||
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Title | Crystal structure of human Nek7 | |||||||||
![]() | Serine/threonine-protein kinase Nek7 | |||||||||
![]() | CELL CYCLE / Kinase | |||||||||
Function / homology | ![]() 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 / : ...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 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 / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nasir, N. / Bayliss, R. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 414 KB | Display | ![]() |
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PDB format | ![]() | 273 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.4 KB | Display | ![]() |
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Full document | ![]() | 475 KB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 49.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s73C ![]() 6s75C ![]() 6sk9C ![]() 6gt1 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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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.) ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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