+Open data
-Basic information
Entry | Database: PDB / ID: 7ojo | |||||||||
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Title | Tankyrase 2 in complex with two small molecule fragments | |||||||||
Components | (Poly [ADP-ribose] polymerase tankyrase- ...) x 2 | |||||||||
Keywords | TRANSFERASE / Inhibitor / Complex / Poly-ADP-ribosylation / Enzyme | |||||||||
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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Sowa, S.T. / Lehtio, L. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: To Be Published Title: Tankyrase 2 in complex with an inhibitor (OM-153) Authors: Sowa, S.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 | 7ojo.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ojo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ojo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ojo_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7ojo_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7ojo_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 7ojo_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/7ojo ftp://data.pdbj.org/pub/pdb/validation_reports/oj/7ojo | HTTPS FTP |
-Related structure data
Related structure data | 5nobS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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:
NCS domain segments:
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Poly [ADP-ribose] polymerase tankyrase- ... , 2 types, 4 molecules AAABBBAB
#1: Protein | Mass: 19482.053 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli) References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases #2: Protein/peptide | Mass: 5364.037 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli) References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases |
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-Non-polymers , 5 types, 161 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris pH=8.5, 200 mM Li2SO4, 24% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→148.88 Å / Num. obs: 21934 / % possible obs: 99.9 % / Redundancy: 24.4 % / CC1/2: 0.981 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 2067 / CC1/2: 0.728 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NOB Resolution: 2.3→74.549 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.862 / SU B: 8.75 / SU ML: 0.201 / Cross valid method: FREE R-VALUE / ESU R: 0.388 / ESU R Free: 0.266 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.737 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→74.549 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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