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- PDB-3epx: Crystal structure of Trypanosoma vivax nucleoside hydrolase in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3epx | ||||||
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Title | Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-2-(hydroxymethyl)-1-(quinolin-8-ylmethyl)pyrrolidin-3,4-diol | ||||||
![]() | IAG-nucleoside hydrolase | ||||||
![]() | HYDROLASE / Rossmann fold / active site loops / aromatic stacking | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing N-glycosyl compounds / nucleobase-containing compound metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Versees, W. / Goeminne, A. / Berg, M. / Vandemeulebroucke, A. / Haemers, A. / Augustyns, K. / Steyaert, J. | ||||||
![]() | ![]() Title: Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors. Authors: Versees, W. / Goeminne, A. / Berg, M. / Vandemeulebroucke, A. / Haemers, A. / Augustyns, K. / Steyaert, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.1 KB | Display | ![]() |
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PDB format | ![]() | 116.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 31.8 KB | Display | |
Data in CIF | ![]() | 48.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3epwC ![]() 1hozS 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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Unit cell |
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Components
#1: Protein | Mass: 37621.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.1 M ammonium sulfate, 0.1 M Bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 18, 2007 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8152 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→72.74 Å / Num. all: 49440 / Num. obs: 49440 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 15.41 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HOZ (with flexible parts removed) Resolution: 1.85→23.33 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.85→23.33 Å
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Refine LS restraints |
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