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- PDB-5ngs: Crystal structure of human MTH1 in complex with inhibitor 6-[(2-p... -
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Basic information
Entry | Database: PDB / ID: 5ngs | |||||||||||||||||||||||||||||||||||||||
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Title | Crystal structure of human MTH1 in complex with inhibitor 6-[(2-phenylethyl)sulfanyl]-7H-purin-2-amine | |||||||||||||||||||||||||||||||||||||||
![]() | 7,8-dihydro-8-oxoguanine triphosphatase | |||||||||||||||||||||||||||||||||||||||
![]() | HYDROLASE / Inhibitor / Fragment / Oxidised nucleotides | |||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() 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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity ...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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / 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 / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / extracellular space / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||
![]() | Gustafsson, R. / Rudling, A. / Almlof, I. / Homan, E. / Scobie, M. / Warpman Berglund, U. / Helleday, T. / Carlsson, J. / Stenmark, P. | |||||||||||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space. Authors: Rudling, A. / Gustafsson, R. / Almlof, I. / Homan, E. / Scobie, M. / Warpman Berglund, U. / Helleday, T. / Stenmark, P. / Carlsson, 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 | ![]() | 84.4 KB | Display | ![]() |
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PDB format | ![]() | 62.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1018.5 KB | Display | ![]() |
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Full document | ![]() | 1022.1 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ngrC ![]() 5ngtC ![]() 3zr1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 3 - 156 / Label seq-ID: 6 - 159
NCS ensembles :
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Components
#1: Protein | Mass: 18253.736 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 5 mmol/L compound and 6 mmol/L MgCl2 were added to MTH1. Sitting drop vapor diffusion experiments at 293K were performed, and MTH1 (9.34 mg/mL) was mixed with reservoir solution (28% (w/v) ...Details: 5 mmol/L compound and 6 mmol/L MgCl2 were added to MTH1. Sitting drop vapor diffusion experiments at 293K were performed, and MTH1 (9.34 mg/mL) was mixed with reservoir solution (28% (w/v) PEG8000, 0.1 mol/L Sodium Acetate pH 4.0 and 0.2 mol/L LiSO4) in a 3:5 ratio. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→28.2 Å / Num. obs: 28944 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1715 / CC1/2: 0.796 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZR1 Resolution: 1.85→28.2 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.04 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.151 / 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: 28.804 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→28.2 Å
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Refine LS restraints |
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