+Open data
-Basic information
Entry | Database: PDB / ID: 2xnn | ||||||
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Title | Structure of Nek2 bound to CCT242430 | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE NEK2 | ||||||
Keywords | TRANSFERASE / CENTROSOME / MITOSIS / CELL CYCLE | ||||||
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: 2.5 Å | ||||||
Authors | Mas-Droux, C. / Bayliss, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Benzimidazole Inhibitors Induce a Dfg-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure-Activity Relationship. Authors: Solanki, S. / Innocenti, P. / Mas-Droux, C. / Boxall, K. / Barillari, C. / Van Montfort, R.L. / Aherne, G.W. / Bayliss, R. / Hoelder, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xnn.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xnn.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 2xnn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xnn_validation.pdf.gz | 803.5 KB | Display | wwPDB validaton report |
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Full document | 2xnn_full_validation.pdf.gz | 807.5 KB | Display | |
Data in XML | 2xnn_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 2xnn_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/2xnn ftp://data.pdbj.org/pub/pdb/validation_reports/xn/2xnn | HTTPS FTP |
-Related structure data
Related structure data | 2xnmC 2xnoC 2xnpC 2w5aS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32662.479 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-271 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL References: UniProt: P51955, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-430 / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / #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: 2.58 Å3/Da / Density % sol: 52.34 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→39.75 Å / Num. obs: 11653 / % possible obs: 99.8 % / Observed criterion σ(I): 6 / Redundancy: 3.2 % / Biso Wilson estimate: 28.56 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W5A Resolution: 2.5→31.243 Å / SU ML: 0.36 / σ(F): 0.08 / Phase error: 23.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.107 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→31.243 Å
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Refine LS restraints |
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LS refinement shell |
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