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Yorodumi- PDB-5v7w: Crystal structure of human PARP14 bound to 2-{[(1-methylpiperidin... -
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-Basic information
Entry | Database: PDB / ID: 5v7w | ||||||
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Title | Crystal structure of human PARP14 bound to 2-{[(1-methylpiperidin-4-yl)methyl]amino}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one inhibitor | ||||||
Components | Poly [ADP-ribose] polymerase 14 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / HUMAN PARP14 / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å | ||||||
Authors | saikatendu, k.s. / Hirozane, M. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Identification of PARP14 inhibitors using novel methods for detecting auto-ribosylation. Authors: Yoneyama-Hirozane, M. / Matsumoto, S.I. / Toyoda, Y. / Saikatendu, K.S. / Zama, Y. / Yonemori, K. / Oonishi, M. / Ishii, T. / Kawamoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v7w.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v7w.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 5v7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/5v7w ftp://data.pdbj.org/pub/pdb/validation_reports/v7/5v7w | HTTPS FTP |
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-Related 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22101.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Production host: Escherichia coli (E. coli) / References: UniProt: Q460N5, 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: 2.95 Å3/Da / Density % sol: 58.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2M Sodium-malonate, pH 7.2-7.8 |
-Data collection
Diffraction | Mean temperature: 277 K / Ambient temp details: CRYO |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.2398 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→72.45 Å / Num. obs: 14247 / % possible obs: 99.88 % / Redundancy: 3.7 % / Net I/σ(I): 9.8 |
-Processing
Software |
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Refinement | Resolution: 2.65→72.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 35.708 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R Free: 0.329 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.378 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→72.45 Å
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