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Yorodumi- PDB-6sgd: Nek2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sgd | |||||||||
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Title | Nek2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhibitor 24 | |||||||||
Components | Serine/threonine-protein kinase Nek2 | |||||||||
Keywords | CELL CYCLE / "covalent inhibitor" 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 / : / Recruitment of NuMA to mitotic centrosomes / positive regulation of telomere maintenance via telomerase / Anchoring of the basal body to the plasma membrane / 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 / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Richards, M.W. / Mas-Droux, C.P. / Bayliss, R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Rsc Med Chem / Year: 2020 Title: 2-Arylamino-6-ethynylpurines are cysteine-targeting irreversible inhibitors of Nek2 kinase. Authors: Matheson, C.J. / Coxon, C.R. / Bayliss, R. / Boxall, K. / Carbain, B. / Fry, A.M. / Hardcastle, I.R. / Harnor, S.J. / Mas-Droux, C. / Newell, D.R. / Richards, M.W. / Sivaprakasam, M. / ...Authors: Matheson, C.J. / Coxon, C.R. / Bayliss, R. / Boxall, K. / Carbain, B. / Fry, A.M. / Hardcastle, I.R. / Harnor, S.J. / Mas-Droux, C. / Newell, D.R. / Richards, M.W. / Sivaprakasam, M. / Turner, D. / Griffin, R.J. / Golding, B.T. / Cano, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sgd.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sgd.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 6sgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sgd_validation.pdf.gz | 754.4 KB | Display | wwPDB validaton report |
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Full document | 6sgd_full_validation.pdf.gz | 760.6 KB | Display | |
Data in XML | 6sgd_validation.xml.gz | 14 KB | Display | |
Data in CIF | 6sgd_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/6sgd ftp://data.pdbj.org/pub/pdb/validation_reports/sg/6sgd | HTTPS FTP |
-Related structure data
Related structure data | 6sghC 6sgiC 6sgkC 2w5hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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 / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P51955, non-specific serine/threonine protein kinase | ||||||
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#2: Chemical | ChemComp-NA / | ||||||
#3: Chemical | #4: Chemical | ChemComp-LD5 / | #5: 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: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris pH 8.5, 3% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / 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→49.75 Å / Num. obs: 21455 / % possible obs: 99.56 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.72 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.067 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3143 / Rpim(I) all: 0.424 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W5H Resolution: 2→30.35 Å / SU ML: 0.2263 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4566
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30.35 Å
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Refine LS restraints |
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LS refinement shell |
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