+Open data
-Basic information
Entry | Database: PDB / ID: 7pw3 | |||||||||
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Title | PARP15 catalytic domain in complex with OUL217 | |||||||||
Components | Protein mono-ADP-ribosyltransferase PARP15 | |||||||||
Keywords | TRANSFERASE / ADP-ribosyltransferase / Inhibitor / Complex | |||||||||
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: 1.4 Å | |||||||||
Authors | Maksimainen, M.M. / Murthy, S. / Lehtio, L. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2022 Title: Potent 2,3-dihydrophthalazine-1,4-dione derivatives as dual inhibitors for mono-ADP-ribosyltransferases PARP10 and PARP15. Authors: Nizi, M.G. / Maksimainen, M.M. / Murthy, S. / Massari, S. / Alaviuhkola, J. / Lippok, B.E. / Sowa, S.T. / Galera-Prat, A. / Prunskaite-Hyyrylainen, R. / Luscher, B. / Korn, P. / Lehtio, L. / Tabarrini, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pw3.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pw3.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 7pw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pw3_validation.pdf.gz | 752.6 KB | Display | wwPDB validaton report |
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Full document | 7pw3_full_validation.pdf.gz | 754.2 KB | Display | |
Data in XML | 7pw3_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 7pw3_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/7pw3 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/7pw3 | HTTPS FTP |
-Related structure data
Related structure data | 7pwaC 7pwcC 7pwkC 7pwlC 7pwmC 7pwpC 7pwqC 7pwrC 7pwsC 7pwuC 7pwwC 7px6C 7px7C 3bljS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.23729/ba2c02ed-340f-4047-94c5-81ccf11100f9 Data set type: diffraction image 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-8C7 / | #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: 2.44 Å3/Da / Density % sol: 49.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium chloride pH 7.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 97254 / % possible obs: 98.3 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rrim(I) all: 0.073 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.4→1.44 Å / Num. unique obs: 7053 / CC1/2: 0.614 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BLJ Resolution: 1.4→43.63 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.728 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 / 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: 81.89 Å2 / Biso mean: 21.421 Å2 / Biso min: 11.03 Å2
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Refinement step | Cycle: final / Resolution: 1.4→43.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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