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- PDB-6oey: Crystal structure of Trypanothione Reductase from Trypanosoma bru... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6oey | ||||||
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Title | Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor (+)-5-{5-[1-(Pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1-{[(2S)-pyrrolidin-2-yl]methyl}-1H-indole | ||||||
![]() | Trypanothione reductase | ||||||
![]() | oxidoreductase/oxidoreductase inhibitor / Trypanosoma / trypanothione / inhibitor / sleeping sickness / OXIDOREDUCTASE / oxidoreductase-oxidoreductase inhibitor complex | ||||||
Function / homology | ![]() trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress ...trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / nucleoplasm / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Halgas, O. / De Gasparo, R. / Harangozo, D. / Krauth-Siegel, R.L. / Diederich, F. / Pai, E.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Targeting a Large Active Site: Structure-Based Design of Nanomolar Inhibitors of Trypanosoma brucei Trypanothione Reductase. Authors: De Gasparo, R. / Halgas, O. / Harangozo, D. / Kaiser, M. / Pai, E.F. / Krauth-Siegel, R.L. / Diederich, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.5 KB | Display | ![]() |
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PDB format | ![]() | 171.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 631.8 KB | Display | ![]() |
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Full document | ![]() | 635.3 KB | Display | |
Data in XML | ![]() | 2.6 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oexC ![]() 6oezC ![]() 4nevS 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 on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 53497.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb10.406.0520 / Plasmid: PET3ATBTRYR Production host: ![]() ![]() Strain (production host): BL21-Gold(DE3)pLysS AG References: UniProt: Q389T8, trypanothione-disulfide reductase |
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-Non-polymers , 5 types, 589 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/M9S.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/M9S.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-M9S / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.5 % / Description: yellowish tetragonal bipyramid |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 microL of protein were mixed with 2 microL of well solution (500 microL; 0.1 M HEPES, pH 7.5, 2.2 M (NH4)2SO4); crystals grew within 2weeks |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→52 Å / Num. obs: 91815 / % possible obs: 99 % / Redundancy: 13.2 % / CC1/2: 0.999 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Num. unique obs: 8473 / CC1/2: 0.598 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NEV Resolution: 2.1→52 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→52 Å
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Refine LS restraints |
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LS refinement shell |
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