+Open data
-Basic information
Entry | Database: PDB / ID: 2w5b | ||||||
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Title | Human Nek2 kinase ATPgammaS-bound | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE NEK2 | ||||||
Keywords | TRANSFERASE / MEIOSIS / MITOSIS / CYTOPLASM / METAL-BINDING / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING / MAGNESIUM / CELL CYCLE / ATP-BINDING / CENTROSOME SPLITTING / CELL DIVISION | ||||||
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 / 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å | ||||||
Authors | Bayliss, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Insights Into the Conformational Variability and Regulation of Human Nek2 Kinase. Authors: Westwood, I. / Cheary, D.M. / Baxter, J.E. / Richards, M.W. / Van Montfort, R.L. / Fry, A.M. / Bayliss, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w5b.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w5b.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 2w5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/2w5b ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w5b | HTTPS FTP |
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-Related 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: 32632.451 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-271 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P51955, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-AGS / | ||
#3: Chemical | ChemComp-CL / | ||
#4: Chemical | ChemComp-MG / | ||
#5: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | C-TERMINAL LEHHHHHH AFFINITY TAG FROM VECTOR SEQUENCE T175A MUTATION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.91 % / Description: NONE |
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Crystal grow | Details: 50 MM TRIS, PH 8.5 2-10% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49 Å / Num. obs: 12943 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 2.5 % / Biso Wilson estimate: 15.71 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.4→49.56 Å / SU ML: 0.36 / σ(F): 0.13 / Phase error: 21.65 / 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: 43.56 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→49.56 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.9491 Å / Origin y: 14.1695 Å / Origin z: -16.2354 Å
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Refinement TLS group | Selection details: CHAIN A |