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Yorodumi- PDB-4l33: Tankyrase 2 in complex with cyanomethyl 4-(4-oxo-4H-chromen-2-yl)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l33 | ||||||
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Title | Tankyrase 2 in complex with cyanomethyl 4-(4-oxo-4H-chromen-2-yl)benzoate | ||||||
Components | (Tankyrase-2) x 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / TRANSFERASE / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Narwal, M. / Haikarainen, T. / Lehtio, L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Discovery of tankyrase inhibiting flavones with increased potency and isoenzyme selectivity. Authors: Narwal, M. / Koivunen, J. / Haikarainen, T. / Obaji, E. / Legala, O.E. / Venkannagari, H. / Joensuu, P. / Pihlajaniemi, T. / Lehtio, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l33.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l33.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 4l33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/4l33 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/4l33 | HTTPS FTP |
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-Related structure data
Related structure data | 4bs4C 4kzlC 4kzqC 4kzuC 4l09C 4l0bC 4l0iC 4l0sC 4l0tC 4l0vC 4l10C 4l2fC 4l2gC 4l2kC 4l31C 4l32C 4l34C 3u9hS 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 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: C-terminal fragment, UNP residues 946-1113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase #2: Protein/peptide | Mass: 5493.216 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 1114-1162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase |
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-Non-polymers , 6 types, 208 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: 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: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Li2SO4, 0.1 M Tris HCl 24 % 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: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 10, 2011 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.3 Å / Num. all: 31344 / Num. obs: 31344 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.75 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2 / Num. unique all: 2290 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U9H Resolution: 2.1→45.3 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.297 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.18 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.948 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→45.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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