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Yorodumi- PDB-3p0p: Human Tankyrase 2 - Catalytic PARP domain in complex with an inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p0p | ||||||
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Title | Human Tankyrase 2 - Catalytic PARP domain in complex with an inhibitor | ||||||
Components | Tankyrase-2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN-LIGAND COMPLEX / Structural Genomics / Structural Genomics Consortium / SGC / DIPHTHERIA TOXIN LIKE FOLD / TRANSFERASE / NAD+ / ADP-RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Sehic, A. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2012 Title: Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Kull, B. / Robertson, G.M. / Pellicciari, R. / Schuler, H. / Weigelt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p0p.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p0p.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 3p0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p0p_validation.pdf.gz | 836.9 KB | Display | wwPDB validaton report |
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Full document | 3p0p_full_validation.pdf.gz | 841 KB | Display | |
Data in XML | 3p0p_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 3p0p_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/3p0p ftp://data.pdbj.org/pub/pdb/validation_reports/p0/3p0p | HTTPS FTP |
-Related structure data
Related structure data | 3goyC 3mhjC 3mhkC 3p0nC 3p0qC 3se2C 3smiC 3smjC 3kr7S S: Starting model for refinement 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
#1: Protein | Mass: 27299.764 Da / Num. of mol.: 2 / Fragment: Catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: 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: 48.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 23% PEG3350, 0.2M ammonium sulfate, 0.1M Tris-HCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54177 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Feb 4, 2010 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54177 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→66 Å / Num. all: 18543 / Num. obs: 18543 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 34.38 Å2 / Rmerge(I) obs: 0.1855 / Rsym value: 0.1186 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.49→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3858 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1813 / Rsym value: 0.4221 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KR7 Resolution: 2.49→24.86 Å / Cor.coef. Fo:Fc: 0.9063 / Cor.coef. Fo:Fc free: 0.8217 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso max: 101.76 Å2 / Biso mean: 25.38 Å2 / Biso min: 2.44 Å2
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Refine analyze | Luzzati coordinate error obs: 0.304 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→24.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.64 Å / Total num. of bins used: 9
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