+Open data
-Basic information
Entry | Database: PDB / ID: 7otf | |||||||||
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Title | PARP15 catalytic domain in complex with OUL213 | |||||||||
Components | Protein mono-ADP-ribosyltransferase PARP15 | |||||||||
Keywords | TRANSFERASE / Inhibitor / Complex / mono-ADP-ribosyl-transferase | |||||||||
Function / homology | Function and homology information protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Maksimainen, M.M. / Lehtio, L. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2021 Title: Analogs of TIQ-A as inhibitors of human mono-ADP-ribosylating PARPs. Authors: Maksimainen, M.M. / Murthy, S. / Sowa, S.T. / Galera-Prat, A. / Rolina, E. / Heiskanen, J.P. / Lehtio, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7otf.cif.gz | 193.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7otf.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 7otf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7otf_validation.pdf.gz | 793.1 KB | Display | wwPDB validaton report |
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Full document | 7otf_full_validation.pdf.gz | 796.3 KB | Display | |
Data in XML | 7otf_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 7otf_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/7otf ftp://data.pdbj.org/pub/pdb/validation_reports/ot/7otf | HTTPS FTP |
-Related structure data
Related structure data | 7oljC 7om1C 7omcC 7oqqC 7ospC 7ossC 7osxC 7othC 7ouwC 7ouxC 3bljS 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: 25439.459 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP15, BAL3 / Production host: Escherichia coli (E. coli) References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-1H9 / | #3: Chemical | ChemComp-DMS / | #4: 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: 2.42 Å3/Da / Density % sol: 49.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium acetate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 122067 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 1 / Net I/σ(I): 23.24 |
Reflection shell | Resolution: 1.3→1.33 Å / Num. unique obs: 8626 / CC1/2: 0.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BLJ Resolution: 1.3→43.61 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.887 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.041 / 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: 90.82 Å2 / Biso mean: 22.038 Å2 / Biso min: 11.83 Å2
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Refinement step | Cycle: final / Resolution: 1.3→43.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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