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Open data
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Basic information
Entry | Database: PDB / ID: 7aom | ||||||
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Title | Structure of NUDT15 in complex with Ganciclovir triphosphate | ||||||
![]() | Nucleotide triphosphate diphosphatase NUDT15 | ||||||
![]() | HYDROLASE / NUDIX hydrolase / antiviral | ||||||
Function / homology | ![]() 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 / xenobiotic catabolic process / regulation of proteasomal protein catabolic process / response to reactive oxygen species / mitotic cell cycle / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rehling, D. / Zhang, S.M. / Helleday, T. / Stenmark, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: NUDT15-mediated hydrolysis limits the efficacy of anti-HCMV drug ganciclovir. Authors: Zhang, S.M. / Rehling, D. / Jemth, A.S. / Throup, A. / Landazuri, N. / Almlof, I. / Gottmann, M. / Valerie, N.C.K. / Borhade, S.R. / Wakchaure, P. / Page, B.D.G. / Desroses, M. / Homan, E.J. ...Authors: Zhang, S.M. / Rehling, D. / Jemth, A.S. / Throup, A. / Landazuri, N. / Almlof, I. / Gottmann, M. / Valerie, N.C.K. / Borhade, S.R. / Wakchaure, P. / Page, B.D.G. / Desroses, M. / Homan, E.J. / Scobie, M. / Rudd, S.G. / Berglund, U.W. / Soderberg-Naucler, C. / Stenmark, P. / Helleday, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.3 KB | Display | ![]() |
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PDB format | ![]() | 114.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7aopC ![]() 5lpgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (0.14557614524, -0.978208803023, -0.148037575045), (-0.974952818709, -0.167274594542, 0.146581756407), (-0.168150489823, 0.122990844005, -0.978058620464)Vector: -31. ...NCS oper: (Code: given Matrix: (0.14557614524, -0.978208803023, -0.148037575045), Vector: |
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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.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: 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: 2.07 Å3/Da / Density % sol: 40.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris pH 8.5, 0.2M sodium acetate, 34% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.5 Å / Num. obs: 23223 / % possible obs: 99.49 % / Redundancy: 12.8 % / Biso Wilson estimate: 25.53 Å2 / CC1/2: 0.972 / CC star: 0.993 / Rmerge(I) obs: 0.1735 / Rrim(I) all: 0.1812 / Net I/av σ(I): 7.66 / Net I/σ(I): 7.66 |
Reflection shell | Resolution: 1.95→2.022 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.7252 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 2217 / CC1/2: 0.873 / CC star: 0.966 / Rrim(I) all: 0.7554 / % possible all: 96.89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LPG Resolution: 1.95→46.5 Å / SU ML: 0.2214 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3155 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: 33.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→46.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.697906181428 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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