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Open data
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Basic information
Entry | Database: PDB / ID: 6tkp | |||||||||
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Title | Tankyrase 2 in complex with an inhibitor (OM-1900) | |||||||||
![]() | Tankyrase-2 | |||||||||
![]() | TRANSFERASE / Inhibitor / Complex / Poly-ADP-ribosylation / Enzyme | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Sowa, S.T. / Lehtio, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Preclinical Lead Optimization of a 1,2,4-Triazole Based Tankyrase Inhibitor. Authors: Waaler, J. / Leenders, R.G.G. / Sowa, S.T. / Alam Brinch, S. / Lycke, M. / Nieczypor, P. / Aertssen, S. / Murthy, S. / Galera-Prat, A. / Damen, E. / Wegert, A. / Nazare, M. / Lehtio, L. / Krauss, 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 | ![]() | 176.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 855.3 KB | Display | ![]() |
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Full document | ![]() | 859.7 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tg4C ![]() 6tkmC ![]() 6tknC ![]() 6tkqC ![]() 6tkrC ![]() 6tksC ![]() 5nobS 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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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains A B) |
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Components
#1: Protein | Mass: 27299.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 7.5-25% PEG 6000, Bicine, pH = 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03285 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 19583 / % possible obs: 99.9 % / Redundancy: 6.505 % / CC1/2: 0.998 / Net I/σ(I): 11.03 |
Reflection shell | Resolution: 2.4→2.46 Å / Num. unique obs: 1441 / CC1/2: 0.801 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NOB Resolution: 2.4→41.658 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.879 / SU B: 8.357 / SU ML: 0.186 / Cross valid method: FREE R-VALUE / ESU R: 0.437 / ESU R Free: 0.26 Details: Hydrogens have been added in their 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: 40.297 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→41.658 Å
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Refine LS restraints |
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LS refinement shell |
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