+Open data
-Basic information
Entry | Database: PDB / ID: 4pnl | ||||||
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Title | Crystal structure of TNKS-2 in complex with DR2313. | ||||||
Components | Tankyrase-2 | ||||||
Keywords | TRANSFERASE / PARP | ||||||
Function / homology | Function and homology information 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 / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ 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 / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Qiu, W. / Lam, R. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Chirgadze, N.Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2. Authors: Qiu, W. / Lam, R. / Voytyuk, O. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Rottapel, R. / Chirgadze, N.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pnl.cif.gz | 199 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pnl.ent.gz | 156.3 KB | Display | PDB format |
PDBx/mmJSON format | 4pnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/4pnl ftp://data.pdbj.org/pub/pdb/validation_reports/pn/4pnl | HTTPS FTP |
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-Related structure data
Related structure data | 4pmlC 4pnmC 4pnnC 4pnqC 4pnrC 4pnsC 4pntC 4tjuC 4tjwC 4tjyC 4tk0C 4tk5C 4tkfC 4tkgC 4tkiC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 25986.291 Da / Num. of mol.: 4 / Fragment: PARP, catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase |
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-Non-polymers , 5 types, 888 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-DRL / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-DMS / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M NaCl, 0.1M Sodium, Hepes buffer at pH7.5, 12-15% iso-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→44.32 Å / Num. obs: 127678 / % possible obs: 87.4 % / Redundancy: 5.65 % / Biso Wilson estimate: 20.07 Å2 / Net I/σ(I): 18.76 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 2.26 % / Rmerge(I) obs: 0.4941 / Mean I/σ(I) obs: 2 / % possible all: 58.8 |
-Processing
Software | Name: BUSTER / Version: 2.10.0 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.5→44.32 Å / Cor.coef. Fo:Fc: 0.9499 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.095 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.093
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Displacement parameters | Biso mean: 27.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.208 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.5→44.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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