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- PDB-3t6y: 5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t6y | ||||||
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Title | 5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / dUTP binding / Nucleus / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() tRNA metabolic process / Interconversion of nucleotide di- and triphosphates / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / DNA replication / magnesium ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. ...Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / Kahnberg, P. / Brun, R. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Johansson, N.G. / Gilbert, I.H. | ||||||
![]() | ![]() Title: Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase. Authors: Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, J.A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / ...Authors: Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, J.A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / Kahnberg, P. / Brun, R. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Johansson, N.G. / Gilbert, I.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.9 KB | Display | ![]() |
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PDB format | ![]() | 81.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3t60C ![]() 3t64C ![]() 3t70C ![]() 1vyqS 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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Unit cell |
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Components
#1: Protein | Mass: 20632.248 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Gene: PF11_0282 / Plasmid: pET26b / Production host: ![]() ![]() #2: Protein/peptide | | Mass: 298.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.2M Ammonium sulphate, 0.2M di-sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2009 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→37.96 Å / Num. all: 19028 / Num. obs: 19028 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.012 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.6→37.96 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VYQ Resolution: 2.6→37.96 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.548 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.942 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→37.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.601→2.668 Å / Total num. of bins used: 20
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