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- PDB-3epw: 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: 3epw | ||||||
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Title | Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-1-[(4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)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 | ![]() | 161.2 KB | Display | ![]() |
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PDB format | ![]() | 122.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3epxC ![]() 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 | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25 % PEG3350, 0.1 M Bis-Tris, 0.2 M MgCl2, 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: MAR CCD 165 mm / Detector: CCD / Date: Jun 23, 2007 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8051 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→26.86 Å / Num. all: 138694 / Num. obs: 138694 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HOZ (with flexible parts removed) Resolution: 1.3→26.86 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.3→26.86 Å
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Refine LS restraints |
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