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Open data
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Basic information
Entry | Database: PDB / ID: 5mze | ||||||
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Title | Crystal structure of mouse MTH1 with 8-oxo-dGTP | ||||||
![]() | 7,8-dihydro-8-oxoguanine triphosphatase | ||||||
![]() | HYDROLASE / substrate / complex | ||||||
Function / homology | ![]() Phosphate bond hydrolysis by NUDT proteins / 2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity ...Phosphate bond hydrolysis by NUDT proteins / 2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to cadmium ion / acrosomal vesicle / male gonad development / nuclear membrane / mitochondrial matrix / mitochondrion / extracellular space / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Narwal, M. / Jemth, A.-S. / Helleday, T. / Stenmark, P. | ||||||
![]() | ![]() Title: Crystal Structures and Inhibitor Interactions of Mouse and Dog MTH1 Reveal Species-Specific Differences in Affinity. Authors: Narwal, M. / Jemth, A.S. / Gustafsson, R. / Almlof, I. / Warpman Berglund, U. / Helleday, T. / Stenmark, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.7 KB | Display | ![]() |
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PDB format | ![]() | 117.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mzfC ![]() 5mzgC ![]() 6ehhC ![]() 3zr1S 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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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 20101.662 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P53368, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase |
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-Non-polymers , 5 types, 419 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/8DG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/8DG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | ChemComp-8DG / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.66 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium nitrate, 34% PEG 3350 and 0.01 M copper (II) chloride dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.29 Å / Num. obs: 51831 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.2 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZR1 Resolution: 2.1→47.29 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.556 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.172 / 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: 23.907 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→47.29 Å
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Refine LS restraints |
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