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- PDB-5nve: Crystal structure of TNKS2 in complex with 2-(4-ethoxyphenyl)-3,4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nve | ||||||
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Title | Crystal structure of TNKS2 in complex with 2-(4-ethoxyphenyl)-3,4-dihydroquinazolin-4-one | ||||||
![]() | (Tankyrase-2) x 2 | ||||||
![]() | TRANSFERASE / Tankyrase / Inhibitor / ARTD6 / PARP5b / ADP-ribosyltransferase | ||||||
Function / homology | ![]() XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nkizinkiko, Y. / Haikarainen, T. / Lehtio, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 2-Phenylquinazolinones as dual-activity tankyrase-kinase inhibitors. Authors: Nkizinkiko, Y. / Desantis, J. / Koivunen, J. / Haikarainen, T. / Murthy, S. / Sancineto, L. / Massari, S. / Ianni, F. / Obaji, E. / Loza, M.I. / Pihlajaniemi, T. / Brea, J. / Tabarrini, O. / Lehtio, L. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.2 KB | Display | ![]() |
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PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nsxC ![]() 5nt0C ![]() 5nt4C ![]() 5nutC ![]() 5nvcC ![]() 5nvfC ![]() 5nvhC ![]() 5nwbC ![]() 5nwcC ![]() 5nwdC ![]() 5nwgC ![]() 5nxeC ![]() 5owsC ![]() 5owtC ![]() 3u9hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABHI
#1: Protein | Mass: 21824.545 Da / Num. of mol.: 2 / Fragment: UNP residues 946-1113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 5493.216 Da / Num. of mol.: 2 / Fragment: UNP residues 1114-1162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 371 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/9AQ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/9AQ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M LISO4, 0.1 M TRIS HCL, 24/26 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953723 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.47 Å / Num. obs: 84984 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.69 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3U9H Resolution: 1.5→45.47 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.345 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.066 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.326 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→45.47 Å
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Refine LS restraints |
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