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Yorodumi- PDB-5lx6: Human PARP10 (ARTD10), catalytic fragment in complex with PARP in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lx6 | ||||||
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Title | Human PARP10 (ARTD10), catalytic fragment in complex with PARP inhibitor Veliparib | ||||||
Components | Poly [ADP-ribose] polymerase 10 | ||||||
Keywords | TRANSFERASE / Transferase domain / ADP-ribosylation / PARP inhibitor | ||||||
Function / homology | Function and homology information negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / negative regulation of NF-kappaB transcription factor activity / K63-linked polyubiquitin modification-dependent protein binding / protein poly-ADP-ribosylation ...negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / negative regulation of NF-kappaB transcription factor activity / K63-linked polyubiquitin modification-dependent protein binding / protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / translesion synthesis / negative regulation of fibroblast proliferation / nucleotidyltransferase activity / transcription corepressor activity / chromatin organization / DNA-binding transcription factor binding / viral protein processing / negative regulation of gene expression / nucleolus / Golgi apparatus / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Karlberg, T. / Thorsell, A.G. / Schuler, H. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors. Authors: Thorsell, A.G. / Ekblad, T. / Karlberg, T. / Low, M. / Pinto, A.F. / Tresaugues, L. / Moche, M. / Cohen, M.S. / Schuler, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lx6.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lx6.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/5lx6 ftp://data.pdbj.org/pub/pdb/validation_reports/lx/5lx6 | HTTPS FTP |
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-Related structure data
Related structure data | 4r5wC 4r6eC 4rv6C 4tvjC 4undC 4uxbC 3hkvS 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: 21628.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP10 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q53GL7, NAD+ ADP-ribosyltransferase #2: Chemical | #3: 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: 3.04 Å3/Da / Density % sol: 59.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 12% PEG3350, 0.1 M Ammonium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 25, 2016 |
Radiation | Monochromator: single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→47.65 Å / Num. obs: 141779 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.6 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HKV Resolution: 1.25→47.65 Å / Cor.coef. Fo:Fc: 0.9379 / Cor.coef. Fo:Fc free: 0.9377 / SU R Cruickshank DPI: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.044 / SU Rfree Blow DPI: 0.042 / SU Rfree Cruickshank DPI: 0.042
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Displacement parameters | Biso mean: 20.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.174 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.25→47.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.28 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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