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Yorodumi- PDB-7lun: Human PARP14 (ARTD8), catalytic fragment in complex with RBN011980 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lun | ||||||
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Title | Human PARP14 (ARTD8), catalytic fragment in complex with RBN011980 | ||||||
Components | Protein mono-ADP-ribosyltransferase PARP14 | ||||||
Keywords | TRANSFERASE/Inhibitor / PARP14 / ARTD8 / monoPARP / ADP ribosylation / inhibitor complex / TRANSFERASE-Inhibitor complex / TRANSFERASE | ||||||
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+-protein poly-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+-protein poly-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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.57 Å | ||||||
Authors | Dorsey, B.W. / Swinger, K.K. / Schenkel, L.B. / Church, W.D. / Perl, N.R. / Vasbinder, M.M. / Wigle, T.J. / Kuntz, K.W. | ||||||
Citation | Journal: Chembiochem / Year: 2021 Title: Targeted Degradation of PARP14 Using a Heterobifunctional Small Molecule. Authors: Wigle, T.J. / Ren, Y. / Molina, J.R. / Blackwell, D.J. / Schenkel, L.B. / Swinger, K.K. / Kuplast-Barr, K. / Majer, C.R. / Church, W.D. / Lu, A.Z. / Mo, J. / Abo, R. / Cheung, A. / Dorsey, B. ...Authors: Wigle, T.J. / Ren, Y. / Molina, J.R. / Blackwell, D.J. / Schenkel, L.B. / Swinger, K.K. / Kuplast-Barr, K. / Majer, C.R. / Church, W.D. / Lu, A.Z. / Mo, J. / Abo, R. / Cheung, A. / Dorsey, B.W. / Niepel, M. / Perl, N.R. / Vasbinder, M.M. / Keilhack, H. / Kuntz, K.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lun.cif.gz | 317.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lun.ent.gz | 260.6 KB | Display | PDB format |
PDBx/mmJSON format | 7lun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/7lun ftp://data.pdbj.org/pub/pdb/validation_reports/lu/7lun | HTTPS FTP |
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-Related structure data
Related structure data | 7l9yC 3smjS 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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Unit cell |
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-Components
#1: Protein | Mass: 22172.574 Da / Num. of mol.: 8 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, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-YFG / #3: Chemical | ChemComp-CL / | #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: 48.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Acetate pH 4.5, 3.0 M Sodium Chloride, 0.2% w/v 2,2'-Thiodiglycolic acid, 0.2% w/v Adipic acid, 0.2% w/v Benzoic acid, 0.2% w/v Oxalic acid anhydrous, 0.2% w/v Terephthalic ...Details: 0.1 M Sodium Acetate pH 4.5, 3.0 M Sodium Chloride, 0.2% w/v 2,2'-Thiodiglycolic acid, 0.2% w/v Adipic acid, 0.2% w/v Benzoic acid, 0.2% w/v Oxalic acid anhydrous, 0.2% w/v Terephthalic acid, 0.02 M HEPES sodium pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→48.53 Å / Num. obs: 52396 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.57→2.65 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2 / Num. unique obs: 4540 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3smj Resolution: 2.57→48.53 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.867 / SU B: 15.618 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 194.55 Å2 / Biso mean: 38.306 Å2 / Biso min: 0.69 Å2
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Refinement step | Cycle: final / Resolution: 2.57→48.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.57→2.637 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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