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Open data
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Basic information
Entry | Database: PDB / ID: 2xk3 | ||||||
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Title | Structure of Nek2 bound to Aminopyrazine compound 35 | ||||||
![]() | SERINE/THREONINE-PROTEIN KINASE NEK2 | ||||||
![]() | TRANSFERASE / CENTROSOME / MITOSIS | ||||||
Function / homology | ![]() 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 / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mas-Droux, C. / Bayliss, R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.2 KB | Display | ![]() |
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PDB format | ![]() | 91.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 710.2 KB | Display | ![]() |
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Full document | ![]() | 713.8 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xk4C ![]() 2xk6C ![]() 2xk7C ![]() 2xk8C ![]() 2xkcC ![]() 2xkdC ![]() 2xkeC ![]() 2xkfC ![]() 2wqoS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: P51955, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-XK3 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % / Description: NONE |
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Crystal grow | Details: 2-10% PEG8000, 100MM TRIS PH6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50.3 Å / Num. obs: 13956 / % possible obs: 81.2 % / Observed criterion σ(I): 6 / Redundancy: 3.4 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WQO Resolution: 2.2→19.684 Å / SU ML: 0.27 / σ(F): 0.03 / Phase error: 23.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.127 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.684 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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