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Yorodumi- PDB-4uvl: Crystal structure of human tankyrase 2 in complex with 5-amino-1,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uvl | ||||||
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Title | Crystal structure of human tankyrase 2 in complex with 5-amino-1,2- dihydroisoquinolin-1-one | ||||||
Components | TANKYRASE-2 | ||||||
Keywords | TRANSFERASE / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / ADP- RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
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 / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Narwal, M. / Haikarainen, T. / Lehtio, L. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2015 Title: Exploration of the Nicotinamide-Binding Site of the Tankyrases, Identifying 3-Arylisoquinolin-1-Ones as Potent and Selective Inhibitors in Vitro. Authors: Paine, H.A. / Nathubhai, A. / Woon, E.C.Y. / Sunderland, P.T. / Wood, P.J. / Mahon, M.F. / Lloyd, M.D. / Thompson, A.S. / Haikarainen, T. / Narwal, M. / Lehtio, L. / Threadgill, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uvl.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uvl.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 4uvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/4uvl ftp://data.pdbj.org/pub/pdb/validation_reports/uv/4uvl | HTTPS FTP |
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-Related structure data
Related structure data | 4uvnC 4uvoC 4uvpC 4uvsC 4uvtC 4uvuC 4uvvC 4uvwC 4uvxC 4uvyC 4uvzC 3kr7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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 , 1 types, 2 molecules AC
#1: Protein | Mass: 27299.764 Da / Num. of mol.: 2 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 946-1162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA 2 / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase |
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-Non-polymers , 5 types, 317 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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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, 22% PEG3350, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07227 |
Detector | Date: Apr 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 36278 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.85 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KR7 Resolution: 2→48.89 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.36 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.161 Å2
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Refinement step | Cycle: LAST / Resolution: 2→48.89 Å
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