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- PDB-5c5r: CRYSTAL STRUCTURE OF HUMAN TANKYRASE-2 IN COMPLEX WITH A PYRANOPY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5c5r | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN TANKYRASE-2 IN COMPLEX WITH A PYRANOPYRIDONE INHIBITOR | ||||||
![]() | (Tankyrase-2) x 2 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / WNT-SIGNALLING / BETA-CATENIN / PARP-DOMAIN / ADP-RIBOSYLATION / AXIN / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lukacs, C.M. / Janson, C.A. | ||||||
![]() | ![]() Title: Fragment-Based Drug Design of Novel Pyranopyridones as Cell Active and Orally Bioavailable Tankyrase Inhibitors. Authors: de Vicente, J. / Tivitmahaisoon, P. / Berry, P. / Bolin, D.R. / Carvajal, D. / He, W. / Huang, K.S. / Janson, C. / Liang, L. / Lukacs, C. / Petersen, A. / Qian, H. / Yi, L. / Zhuang, Y. / Hermann, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114 KB | Display | ![]() |
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PDB format | ![]() | 85.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5c5pC ![]() 5c5qC ![]() 3kr8S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#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 , 4 types, 529 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/0E1.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/0E1.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30-40% PEG 3350, 5% SATURATED AMMONIUM SULFATE, 0.1M TRIS PH 8.5 PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→49 Å / Num. obs: 77657 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.3 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KR8 Resolution: 1.55→49 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2156381.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.77 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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