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Yorodumi- PDB-7kkn: Structure of the catalytic domain of tankyrase 1 in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kkn | ||||||
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Title | Structure of the catalytic domain of tankyrase 1 in complex with talazoparib | ||||||
Components | Poly [ADP-ribose] polymerase | ||||||
Keywords | TRANSFERASE / PARP1 | ||||||
Function / homology | Function and homology information negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / 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 ...negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / 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 / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / mRNA transport / spindle assembly / nuclear pore / : / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / mitotic spindle organization / TCF dependent signaling in response to WNT / Degradation of AXIN / peptidyl-threonine phosphorylation / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / protein transport / positive regulation of canonical Wnt signaling pathway / histone binding / peptidyl-serine phosphorylation / nuclear membrane / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / cell division / Golgi membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Gajiwala, K.S. / Ryan, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Dissecting the molecular determinants of clinical PARP1 inhibitor selectivity for tankyrase1. Authors: Ryan, K. / Bolanos, B. / Smith, M. / Palde, P.B. / Cuenca, P.D. / VanArsdale, T.L. / Niessen, S. / Zhang, L. / Behenna, D. / Ornelas, M.A. / Tran, K.T. / Kaiser, S. / Lum, L. / Stewart, A. / Gajiwala, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kkn.cif.gz | 203.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kkn.ent.gz | 160.6 KB | Display | PDB format |
PDBx/mmJSON format | 7kkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kkn_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7kkn_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7kkn_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 7kkn_validation.cif.gz | 62.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/7kkn ftp://data.pdbj.org/pub/pdb/validation_reports/kk/7kkn | HTTPS FTP |
-Related structure data
Related structure data | 7kk2C 7kk3C 7kk4C 7kk5C 7kk6C 7kkmC 7kkoC 7kkpC 7kkqC 2rf5S 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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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 24356.580 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: Q59FX0, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-2YQ / ( #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.37 Å3/Da / Density % sol: 48.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: Buffer: 0.1 M MES (pH 6.50) Precipitant: 15.0 %w/v PEG 8000 Precipitant: 40.0 %v/v iso-propanol |
-Data collection
Diffraction | Mean temperature: 98 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→83.3 Å / Num. obs: 110073 / % possible obs: 87.1 % / Redundancy: 3.1 % / CC1/2: 0.998 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.48→1.608 Å / Num. unique obs: 5453 / CC1/2: 0.606 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2rf5 Resolution: 1.48→21.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.101 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.094
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Displacement parameters | Biso max: 99.5 Å2 / Biso mean: 22.68 Å2 / Biso min: 4.06 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.48→21.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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