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Open data
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Basic information
Entry | Database: PDB / ID: 7f41 | ||||||
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Title | PARP15 catalytic domain in complex with 3-AMINOBENZAMIDE | ||||||
![]() | Protein mono-ADP-ribosyltransferase PARP15 | ||||||
![]() | TRANSFERASE / Glycosyltransferase / NAD / mono-ADP-ribosyltransferase | ||||||
Function / homology | ![]() protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J. | ||||||
![]() | ![]() Title: PARP15 catalytic domain in complex with 3-AMINOBENZAMIDE Authors: Zhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.1 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 763.9 KB | Display | ![]() |
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Full document | ![]() | 765.9 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bljS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22749.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-3AB / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100mM HEPES buffer,pH6.5, 22%PEG 3350, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.39721383763→27.3402061526 Å / Num. obs: 874703 / % possible obs: 85.8 % / Redundancy: 10.3 % / Biso Wilson estimate: 13.1309538906 Å2 / Rsym value: 0.083 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 1.4→1.43 Å / Num. unique obs: 84652 / Rsym value: 0.993 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BLJ Resolution: 1.39721383763→27.3402061526 Å / SU ML: 0.137939977293 / Cross valid method: NONE / σ(F): 1.35937084149 / Phase error: 22.1125552579 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.1818679805 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39721383763→27.3402061526 Å
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Refine LS restraints |
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LS refinement shell |
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