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- PDB-3gep: Human hypoxanthine guanine phosphoribosyltranserfase in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gep | ||||||
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Title | Human hypoxanthine guanine phosphoribosyltranserfase in complex with (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)guanine | ||||||
![]() | Hypoxanthine-guanine phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / phosphoribosyltransferase / acyclic nucleoside phosphonate / purine salvage pathway / malarial chemotherapeutic / Acetylation / Cytoplasm / Disease mutation / Glycosyltransferase / Gout / Magnesium / Metal-binding / Purine salvage | ||||||
Function / homology | ![]() adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / cerebral cortex neuron differentiation / hypoxanthine salvage / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / cerebral cortex neuron differentiation / hypoxanthine salvage / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / IMP metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / Purine salvage / GMP salvage / IMP 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Guddat, L.W. / Keough, D.T. / Jersey, J. | ||||||
![]() | ![]() Title: Inhibition of hypoxanthine-guanine phosphoribosyltransferase by acyclic nucleoside phosphonates: a new class of antimalarial therapeutics. Authors: Keough, D.T. / Hockova, D. / Holy, A. / Naesens, L.M. / Skinner-Adams, T.S. / Jersey, J. / Guddat, L.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99 KB | Display | ![]() |
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PDB format | ![]() | 76.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1006.3 KB | Display | ![]() |
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Full document | ![]() | 1018.2 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ggcC ![]() 3ggjC ![]() 1z7gS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 24481.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00492, hypoxanthine phosphoribosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M citrate, 10% isopropanol, 29% PEG 4000, 3.9mM (RS)- HPMPG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 5, 2007 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.63 Å / Num. all: 13343 / Num. obs: 13343 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1334 / Rsym value: 0.179 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Z7G Resolution: 2.6→29.63 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 45.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→29.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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