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Yorodumi- PDB-4l7r: Human artd3 (parp3) - catalytic domain in complex with inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l7r | ||||||
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Title | Human artd3 (parp3) - catalytic domain in complex with inhibitor ME0400 | ||||||
Components | Poly [ADP-ribose] polymerase 3 | ||||||
Keywords | transferase/transferase inhibitor / DIPHTHERIA TOXIN LIKE ADP-RIBOSE TRANSFERASE / TRANSFERASE / ADP-RIBOSYLATION / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information 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 / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic activity / regulation of mitotic spindle organization / centriole / nucleotidyltransferase activity / telomere maintenance / double-strand break repair / site of double-strand break / nuclear body / centrosome / nucleolus / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Karlberg, T. / Thorsell, A.G. / Lindgren, A.E.G. / Ekblad, T. / Spjut, S. / Andersson, C.D. / Weigelt, J. / Linusson, A. / Elofsson, M. / Schuler, H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l7r.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l7r.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 4l7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/4l7r ftp://data.pdbj.org/pub/pdb/validation_reports/l7/4l7r | HTTPS FTP |
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-Related structure data
Related structure data | 4l6zC 4l70C 4l7lC 4l7nC 4l7oC 4l7pC 4l7uC 4gv4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: ADPRT3, ADPRTL3, PARP3 / Plasmid: PNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 PRARE / References: UniProt: Q9Y6F1, NAD+ ADP-ribosyltransferase |
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#2: Chemical | ChemComp-M00 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8M 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 2, 2012 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 16348 / Num. obs: 16348 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 30.33 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.092 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1177 / Rsym value: 0.425 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GV4 Resolution: 2.2→27.08 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9059 / SU R Cruickshank DPI: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.252 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→27.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.35 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 18.6163 Å / Origin y: 0.4905 Å / Origin z: 11.8209 Å
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Refinement TLS group | Selection details: { A|177 - A|532 } |