+Open data
-Basic information
Entry | Database: PDB / ID: 5m55 | ||||||
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Title | Nek2 bound to arylaminopurine 71 | ||||||
Components | Serine/threonine-protein kinase Nek2 | ||||||
Keywords | TRANSFERASE / protein kinase / inhibitor / centrosome separation | ||||||
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: 2.4 Å | ||||||
Authors | Bayliss, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Oncotarget / Year: 2017 Title: Structure-guided design of purine-based probes for selective Nek2 inhibition. Authors: Coxon, C.R. / Wong, C. / Bayliss, R. / Boxall, K. / Carr, K.H. / Fry, A.M. / Hardcastle, I.R. / Matheson, C.J. / Newell, D.R. / Sivaprakasam, M. / Thomas, H. / Turner, D. / Yeoh, S. / Wang, ...Authors: Coxon, C.R. / Wong, C. / Bayliss, R. / Boxall, K. / Carr, K.H. / Fry, A.M. / Hardcastle, I.R. / Matheson, C.J. / Newell, D.R. / Sivaprakasam, M. / Thomas, H. / Turner, D. / Yeoh, S. / Wang, L.Z. / 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 | 5m55.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m55.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m55_validation.pdf.gz | 736.3 KB | Display | wwPDB validaton report |
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Full document | 5m55_full_validation.pdf.gz | 739 KB | Display | |
Data in XML | 5m55_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 5m55_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/5m55 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/5m55 | HTTPS FTP |
-Related structure data
Related structure data | 5m51C 5m53C 5m57C 2w5aS 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
#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-7GG / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3 % PEG 8000, 50 mM Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 13101 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W5A Resolution: 2.4→36.683 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→36.683 Å
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Refine LS restraints |
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LS refinement shell |
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