+Open data
-Basic information
Entry | Database: PDB / ID: 7z1y | ||||||||||||
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Title | PARP15 catalytic domain in complex with OUL245 | ||||||||||||
Components | Protein mono-ADP-ribosyltransferase PARP15 | ||||||||||||
Keywords | TRANSFERASE / PARP / 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: 1.75 Å | ||||||||||||
Authors | Maksimainen, M.M. / Lehtio, L. | ||||||||||||
Funding support | Finland, 3items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: [1,2,4]Triazolo[3,4- b ]benzothiazole Scaffold as Versatile Nicotinamide Mimic Allowing Nanomolar Inhibition of Different PARP Enzymes. Authors: Murthy, S. / Nizi, M.G. / Maksimainen, M.M. / Massari, S. / Alaviuhkola, J. / Lippok, B.E. / Vagaggini, C. / Sowa, S.T. / Galera-Prat, A. / Ashok, Y. / Venkannagari, H. / Prunskaite- ...Authors: Murthy, S. / Nizi, M.G. / Maksimainen, M.M. / Massari, S. / Alaviuhkola, J. / Lippok, B.E. / Vagaggini, C. / Sowa, S.T. / Galera-Prat, A. / Ashok, Y. / Venkannagari, H. / Prunskaite-Hyyrylainen, R. / Dreassi, E. / Luscher, B. / Korn, P. / Tabarrini, O. / Lehtio, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z1y.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z1y.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 7z1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z1y_validation.pdf.gz | 695 KB | Display | wwPDB validaton report |
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Full document | 7z1y_full_validation.pdf.gz | 696.5 KB | Display | |
Data in XML | 7z1y_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 7z1y_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/7z1y ftp://data.pdbj.org/pub/pdb/validation_reports/z1/7z1y | HTTPS FTP |
-Related structure data
Related structure data | 7r3lC 7r3oC 7r3zC 7r4aC 7r59C 7r5dC 7r5xC 7z1vC 7z1wC 7z2oC 7z2qC 7z41C 3bljS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.23729/0b11fe27-a545-48b0-a953-292d1e1e1d38 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-I5F / [ | #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: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride pH 7.5, 16-20% 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: 0.96546 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96546 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 50369 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.998 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.75→1.8 Å / Num. unique obs: 3652 / CC1/2: 0.747 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BLJ Resolution: 1.75→43.53 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.495 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.124 / 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: 84.41 Å2 / Biso mean: 26.196 Å2 / Biso min: 13.02 Å2
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Refinement step | Cycle: final / Resolution: 1.75→43.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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