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Yorodumi- PDB-7scr: Crystal structure of trypanosome brucei hypoxanthine-guanine-xant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7scr | ||||||
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Title | Crystal structure of trypanosome brucei hypoxanthine-guanine-xanthine phosphoribzosyltransferase in complex with (4S,7S)-7-hydroxy-4-((guanin-9-yl)methyl)-2,5-dioxaheptan-1,7-diphosphonate | ||||||
Components | Hypoxanthine-guanine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE/INHIBITOR / purine salvage / inhibitor / phosphonate / drug lead / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information xanthine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / glycosome / phosphate ion binding / magnesium ion binding ...xanthine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / glycosome / phosphate ion binding / magnesium ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12068485322 Å | ||||||
Authors | Guddat, L.W. / Keough, D.T. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Stereo-Defined Acyclic Nucleoside Phosphonates are Selective and Potent Inhibitors of Parasite 6-Oxopurine Phosphoribosyltransferases. Authors: Klejch, T. / Keough, D.T. / King, G. / Dolezelova, E. / Cesnek, M. / Budesinsky, M. / Zikova, A. / Janeba, Z. / Guddat, L.W. / Hockova, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7scr.cif.gz | 354.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7scr.ent.gz | 231.4 KB | Display | PDB format |
PDBx/mmJSON format | 7scr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/7scr ftp://data.pdbj.org/pub/pdb/validation_reports/sc/7scr | HTTPS FTP |
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-Related structure data
Related structure data | 7sanC 7sb7C 6mxcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30590.955 Da / Num. of mol.: 6 / Mutation: F49V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb10.70.6660 / Production host: Escherichia coli (E. coli) References: UniProt: Q38CA1, hypoxanthine phosphoribosyltransferase #2: Chemical | ChemComp-8QI / ({( #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.08 Å3/Da / Density % sol: 40.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris propane, 0.2 M lithium sulfate, 17.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→46.41 Å / Num. obs: 83246 / % possible obs: 96.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 28.9731619465 Å2 / CC1/2: 0.97 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.12→2.23 Å / Redundancy: 6.5 % / Num. unique obs: 9413 / CC1/2: 0.75 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6MXC Resolution: 2.12068485322→46.4 Å / SU ML: 0.333984735807 / Cross valid method: FREE R-VALUE / σ(F): 1.33787516497 / Phase error: 32.691214675
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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: 36.648747756 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12068485322→46.4 Å
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Refine LS restraints |
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LS refinement shell |
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