+Open data
-Basic information
Entry | Database: PDB / ID: 7b7v | ||||||
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Title | Structure of NUDT15 in complex with Acyclovir monophosphate | ||||||
Components | Probable 8-oxo-dGTP diphosphatase NUDT15 | ||||||
Keywords | HYDROLASE / Nucleoside Triphosphate Pyrophosphohydrolase / complex / antiviral HYDROLASE | ||||||
Function / homology | Function and homology information nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection ...nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / Azathioprine ADME / regulation of proteasomal protein catabolic process / xenobiotic catabolic process / response to reactive oxygen species / mitotic cell cycle / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Rehling, D. / Stenmark, P. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: NUDT15 polymorphism influences the metabolism and therapeutic effects of acyclovir and ganciclovir. Authors: Nishii, R. / Mizuno, T. / Rehling, D. / Smith, C. / Clark, B.L. / Zhao, X. / Brown, S.A. / Smart, B. / Moriyama, T. / Yamada, Y. / Ichinohe, T. / Onizuka, M. / Atsuta, Y. / Yang, L. / Yang, ...Authors: Nishii, R. / Mizuno, T. / Rehling, D. / Smith, C. / Clark, B.L. / Zhao, X. / Brown, S.A. / Smart, B. / Moriyama, T. / Yamada, Y. / Ichinohe, T. / Onizuka, M. / Atsuta, Y. / Yang, L. / Yang, W. / Thomas, P.G. / Stenmark, P. / Kato, M. / Yang, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b7v.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b7v.ent.gz | 117.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/7b7v ftp://data.pdbj.org/pub/pdb/validation_reports/b7/7b7v | HTTPS FTP |
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-Related structure data
Related structure data | 5lpgS 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: 18635.002 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT15, MTH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NV35, nucleotide diphosphatase #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: 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: 2.08 Å3/Da / Density % sol: 40.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris pH 8.5, 0.2 M MgCl2, 34% PEG 4000 in a 1:2 ratio |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→44.09 Å / Num. obs: 41732 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 25.08 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 2014 / CC1/2: 0.639 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LPG Resolution: 1.6→44.09 Å / SU ML: 0.1761 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3679 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: 34.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→44.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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