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Yorodumi- PDB-6ry4: PARP15 catalytic domain in complex with 4-(3-carbamoylphenoxy)ben... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ry4 | ||||||
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Title | PARP15 catalytic domain in complex with 4-(3-carbamoylphenoxy)benzamide. | ||||||
Components | Protein mono-ADP-ribosyltransferase PARP15 | ||||||
Keywords | PROTEIN BINDING / Inhibitor / Mono-ADP ribosyltransferase.. | ||||||
Function / homology | Function and homology information protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / NAD+ 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: 1.95 Å | ||||||
Authors | Murthy, S.N. / Maksimainen, M.M. / Lehtio, L. | ||||||
Funding support | Finland, 1items
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Citation | Journal: Chemistryopen / Year: 2021 Title: Evaluation of 3- and 4-Phenoxybenzamides as Selective Inhibitors of the Mono-ADP-Ribosyltransferase PARP10. Authors: Korn, P. / Classen, A. / Murthy, S. / Guareschi, R. / Maksimainen, M.M. / Lippok, B.E. / Galera-Prat, A. / Sowa, S.T. / Voigt, C. / Rossetti, G. / Lehtio, L. / Bolm, C. / Luscher, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ry4.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ry4.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ry4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/6ry4 ftp://data.pdbj.org/pub/pdb/validation_reports/ry/6ry4 | HTTPS FTP |
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-Related structure data
Related structure data | 6ek2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22635.408 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-KMW / | #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: 2.79 Å3/Da / Density % sol: 55.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NH4Cl pH 7.5, 18% PEG 3350 / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 26517 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.051 / Rrim(I) all: 0.12 / Χ2: 0.97 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 2756 / Rrim(I) all: 0.76 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EK2 Resolution: 1.95→43.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.399 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.135 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.539 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→43.77 Å
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