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Yorodumi- PDB-4j3m: Tankyrase 2 in complex with 3-chloro-4-(4-methyl-2-oxo-1,2-dihydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j3m | ||||||
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Title | Tankyrase 2 in complex with 3-chloro-4-(4-methyl-2-oxo-1,2-dihydroquinolin-7-yl)benzoic acid | ||||||
Components | Tankyrase-2 | ||||||
Keywords | TRANSFERASE / ribosylation | ||||||
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: 1.9 Å | ||||||
Authors | Jansson, A.E. / Larsson, E.A. / Nordlund, P.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Fragment-based ligand design of novel potent inhibitors of tankyrases. Authors: Larsson, E.A. / Jansson, A.E. / Ng, F.M. / Then, S.W. / Panicker, R. / Liu, B. / Sangthongpitag, K. / Pendharkar, V. / Tai, S.J. / Hill, J. / Dan, C. / Ho, S.Y. / Cheong, W.W. / Poulsen, A. ...Authors: Larsson, E.A. / Jansson, A.E. / Ng, F.M. / Then, S.W. / Panicker, R. / Liu, B. / Sangthongpitag, K. / Pendharkar, V. / Tai, S.J. / Hill, J. / Dan, C. / Ho, S.Y. / Cheong, W.W. / Poulsen, A. / Blanchard, S. / Lin, G.R. / Alam, J. / Keller, T.H. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j3m.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j3m.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 4j3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/4j3m ftp://data.pdbj.org/pub/pdb/validation_reports/j3/4j3m | HTTPS FTP |
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-Related structure data
Related structure data | 3w51C 4iueC 4j1zC 4j21C 4j22C 4j3lC 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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23993.195 Da / Num. of mol.: 2 / Fragment: cataltytic domain, UNP RESIDUES 952-1161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP5B, TANK2, TNKL, TNKS2 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase |
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-Non-polymers , 5 types, 425 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-GOL / | #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: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 17% PEG 3350, 0.2M Ammonium sulphate, 0.1M Tris pH 8.5, vapour diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 40482 / Num. obs: 40482 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KR7 Resolution: 1.9→29.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.704 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 433.58 Å2 / Biso mean: 23.9644 Å2 / Biso min: 7.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.98 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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