+Open data
-Basic information
Entry | Database: PDB / ID: 2xkd | ||||||
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Title | Structure of Nek2 bound to aminopyrazine compound 12 | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE NEK2 | ||||||
Keywords | TRANSFERASE / CENTROSOME / MITOSIS | ||||||
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 / positive regulation of telomerase activity / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of telomere maintenance via telomerase / 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Mas-Droux, C. / Bayliss, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Aminopyrazine Inhibitors Binding to an Unusual Inactive Conformation of the Mitotic Kinase Nek2: Sar and Structural Characterization. Authors: Whelligan, D.K. / Solanki, S. / Taylor, D. / Thomson, D.W. / Cheung, K.M. / Boxall, K. / Mas-Droux, C. / Barillari, C. / Burns, S. / Grummitt, C.G. / Collins, I. / Van Montfort, R.L. / ...Authors: Whelligan, D.K. / Solanki, S. / Taylor, D. / Thomson, D.W. / Cheung, K.M. / Boxall, K. / Mas-Droux, C. / Barillari, C. / Burns, S. / Grummitt, C.G. / Collins, I. / 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 | 2xkd.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xkd.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/2xkd ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xkd | HTTPS FTP |
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-Related structure data
Related structure data | 2xk3C 2xk4C 2xk6C 2xk7C 2xk8C 2xkcC 2xkeC 2xkfC 2wqoS 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: CATALYTIC DOMAIN, RESIDUES 1-271 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P51955, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-T3M / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.94 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→49.95 Å / Num. obs: 21360 / % possible obs: 89.6 % / Observed criterion σ(I): 6 / Redundancy: 3.5 % / Biso Wilson estimate: 24.13 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 4.4 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WQO Resolution: 1.96→31.289 Å / SU ML: 0.2 / σ(F): 0.03 / Phase error: 20.69 / 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: 45.755 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.96→31.289 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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