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Yorodumi- PDB-4kn6: Crystal structure of human hypoxanthine-guanine phosphoribosyltra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kn6 | ||||||
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Title | Crystal structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with 6-fluoro-3-hydroxy-2-pyrazinecarboxamide (T-705) ribose-5'-monophosphate | ||||||
Components | Hypoxanthine-guanine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Favipiravir / 6-oxopurine phosphoribosyltransferase | ||||||
Function / homology | Function and homology information adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / IMP metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / IMP salvage / Purine salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / Azathioprine ADME / purine ribonucleoside salvage / dendrite morphogenesis / dopamine metabolic process / central nervous system neuron development / response to amphetamine / locomotory behavior / T cell mediated cytotoxicity / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.728 Å | ||||||
Authors | Naesens, L. / Guddat, L. / Keough, D. / van Kuilenburg, A.B.P. / Meijer, J. / Vande Voorde, J. / Balzarini, J. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2013 Title: Role of human hypoxanthine Guanine phosphoribosyltransferase in activation of the antiviral agent T-705 (favipiravir). Authors: Naesens, L. / Guddat, L.W. / Keough, D.T. / van Kuilenburg, A.B. / Meijer, J. / Vande Voorde, J. / Balzarini, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kn6.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kn6.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 4kn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/4kn6 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/4kn6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24410.139 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT1, HPRT / Production host: Escherichia coli (E. coli) References: UniProt: P00492, hypoxanthine phosphoribosyltransferase |
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#2: Chemical | ChemComp-1RP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.01 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M sodium chloride, 1 M sodium/potassium tartrate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 14, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.728→43.06 Å / Num. all: 5283 / Num. obs: 5283 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Highest resolution: 2.728 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.728→43.057 Å / SU ML: 0.45 / σ(F): 1.37 / Phase error: 28.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.728→43.057 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -1.4941 Å / Origin y: -15.3217 Å / Origin z: -12.573 Å
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Refinement TLS group | Selection details: all |