+Open data
-Basic information
Entry | Database: PDB / ID: 5nhy | ||||||
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Title | BAY-707 in complex with MTH1 | ||||||
Components | 7,8-dihydro-8-oxoguanine triphosphatase | ||||||
Keywords | HYDROLASE / NUDIX / NUCLEOTIDE HYDROLASE / INHIBITOR / ONCOLOGY | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Ellermann, M. / Eheim, A. / Giese, A. / Bunse, S. / Nowak-Reppel, K. / Neuhaus, R. / Weiske, J. / Quanz, M. / Glasauer, A. / Meyer, H. ...Ellermann, M. / Eheim, A. / Giese, A. / Bunse, S. / Nowak-Reppel, K. / Neuhaus, R. / Weiske, J. / Quanz, M. / Glasauer, A. / Meyer, H. / Queisser, N. / Irlbacher, H. / Bader, B. / Rahm, F. / Viklund, J. / Andersson, M. / Ericsson, U. / Ginman, T. / Forsblom, R. / Lindstrom, J. / Silvander, C. / Tresaugues, L. / Gorjanacz, M. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Novel Class of Potent and Cellularly Active Inhibitors Devalidates MTH1 as Broad-Spectrum Cancer Target. Authors: Ellermann, M. / Eheim, A. / Rahm, F. / Viklund, J. / Guenther, J. / Andersson, M. / Ericsson, U. / Forsblom, R. / Ginman, T. / Lindstrom, J. / Silvander, C. / Tresaugues, L. / Giese, A. / ...Authors: Ellermann, M. / Eheim, A. / Rahm, F. / Viklund, J. / Guenther, J. / Andersson, M. / Ericsson, U. / Forsblom, R. / Ginman, T. / Lindstrom, J. / Silvander, C. / Tresaugues, L. / Giese, A. / Bunse, S. / Neuhaus, R. / Weiske, J. / Quanz, M. / Glasauer, A. / Nowak-Reppel, K. / Bader, B. / Irlbacher, H. / Meyer, H. / Queisser, N. / Bauser, M. / Haegebarth, A. / Gorjanacz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nhy.cif.gz | 147.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nhy.ent.gz | 116.2 KB | Display | PDB format |
PDBx/mmJSON format | 5nhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nhy_validation.pdf.gz | 967.9 KB | Display | wwPDB validaton report |
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Full document | 5nhy_full_validation.pdf.gz | 969.8 KB | Display | |
Data in XML | 5nhy_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5nhy_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/5nhy ftp://data.pdbj.org/pub/pdb/validation_reports/nh/5nhy | HTTPS FTP |
-Related structure data
Related structure data | 3q93S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18253.736 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Full length human MTH1 Isoform p18 containing residuals from a thrombin-cleavage site in N-terminus Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Variant: Isoform p18 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta phage resistant References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.24 Å3/Da / Density % sol: 45.12 % / Description: Long and large rods |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 22.7% PEG4000, 0.24 ammonium sulfate, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2017 / Details: mirrors |
Radiation | Monochromator: Silicon (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→48.19 Å / Num. obs: 35361 / % possible obs: 99.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 30.882 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.032 / Rrim(I) all: 0.074 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.298 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1844 / CC1/2: 0.612 / Rpim(I) all: 0.603 / Rrim(I) all: 1.435 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q93 Resolution: 1.72→48.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.498 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.132 / 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: 42.157 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→48.19 Å
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