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Yorodumi- PDB-6fym: Human PARP14 (ARTD8), catalytic fragment in complex with inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fym | ||||||
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Title | Human PARP14 (ARTD8), catalytic fragment in complex with inhibitor ITK1 | ||||||
Components | Poly [ADP-ribose] polymerase 14 | ||||||
Keywords | TRANSFERASE / ADP-RIBOSYLATION / INHIBITOR COMPLEX / TRANSFERASE DOMAIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Karlberg, T. / Thorsell, A.G. / Kirby, I.T. / Sreenivasan, R. / Cohen, M.S. / Schuler, H. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2018 Title: A Potent and Selective PARP11 Inhibitor Suggests Coupling between Cellular Localization and Catalytic Activity. Authors: Kirby, I.T. / Kojic, A. / Arnold, M.R. / Thorsell, A.G. / Karlberg, T. / Vermehren-Schmaedick, A. / Sreenivasan, R. / Schultz, C. / Schuler, H. / Cohen, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fym.cif.gz | 315.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fym.ent.gz | 259 KB | Display | PDB format |
PDBx/mmJSON format | 6fym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/6fym ftp://data.pdbj.org/pub/pdb/validation_reports/fy/6fym | HTTPS FTP |
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-Related structure data
Related structure data | 6fzmC 4f1lS 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: 22118.590 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase #2: Chemical | ChemComp-EBB / #3: Chemical | #4: 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: 2.74 Å3/Da / Density % sol: 55.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% Poly(ethylene glycol) 3350, 0.2M sodium nitrate |
-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 6M-F / Detector: PIXEL / Date: Jan 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→36.68 Å / Num. obs: 47400 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 41.49 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.068 / Rrim(I) all: 0.13 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3487 / CC1/2: 0.513 / Rpim(I) all: 0.71 / Rrim(I) all: 1.359 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F1L Resolution: 2.15→36.68 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.281 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.213
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Displacement parameters | Biso mean: 46.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→36.68 Å
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LS refinement shell | Resolution: 2.15→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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