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- PDB-4l7l: Human artd3 (parp3) - catalytic domain in complex with inhibitor ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l7l | ||||||
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Title | Human artd3 (parp3) - catalytic domain in complex with inhibitor ME0368 | ||||||
![]() | Poly [ADP-ribose] polymerase 3 | ||||||
![]() | transferase/transferase inhibitor / DIPHTHERIA TOXIN LIKE ADP-RIBOSE TRANSFERASE / TRANSFERASE / ADP-RIBOSYLATION / transferase-transferase inhibitor complex | ||||||
Function / homology | ![]() negative regulation of isotype switching / : / NAD+-protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation ...negative regulation of isotype switching / : / NAD+-protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation / intercellular bridge / positive regulation of double-strand break repair via nonhomologous end joining / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / catalytic activity / regulation of mitotic spindle organization / centriole / telomere maintenance / nucleotidyltransferase activity / double-strand break repair / site of double-strand break / nuclear body / centrosome / nucleolus / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karlberg, T. / Thorsell, A.G. / Lindgren, A.E.G. / Ekblad, T. / Spjut, S. / Andersson, C.D. / Weigelt, J. / Linusson, A. / Elofsson, M. / Schuler, H. | ||||||
![]() | ![]() Title: Chemical Probes to Study ADP-Ribosylation: Synthesis and Biochemical Evaluation of Inhibitors of the Human ADP-Ribosyltransferase ARTD3/PARP3. Authors: Lindgren, A.E. / Karlberg, T. / Ekblad, T. / Spjut, S. / Thorsell, A.G. / Andersson, C.D. / Nhan, T.T. / Hellsten, V. / Weigelt, J. / Linusson, A. / Schuler, H. / Elofsson, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.5 KB | Display | ![]() |
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PDB format | ![]() | 115.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 742.8 KB | Display | ![]() |
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Full document | ![]() | 743.8 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4l6zC ![]() 4l70C ![]() 4l7nC ![]() 4l7oC ![]() 4l7pC ![]() 4l7rC ![]() 4l7uC ![]() 4gv4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39752.074 Da / Num. of mol.: 1 / Fragment: Catalytic PARP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-1VA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.95M DL-Malic Acid, 0.1M Bis-tris-propane , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2011 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 18469 / Num. obs: 18469 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.132 / Rsym value: 0.142 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1088 / Rsym value: 0.625 / % possible all: 78.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4GV4 Resolution: 2.1→28.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.094 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.257 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.637 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→28.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.768 Å / Origin y: 0.496 Å / Origin z: 11.734 Å
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