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- PDB-6rb5: Trypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rb5 | ||||||
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Title | Trypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-6,6-dimethylbicyclo[3.1.1]heptan-2-yl)ethyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl)propyl)(methyl)amino)methyl)-4-hydroxypiperidine-1-carboximidamide | ||||||
![]() | Trypanothione reductase | ||||||
![]() | OXIDOREDUCTASE / TRYPANOTHIONE METABOLISM / ANTIOXIDANT / TRYPANOSOMA BRUCEI | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Ilari, A. / Fiorillo, A. / Battista, T. / Mocci, S. | ||||||
![]() | ![]() Title: Spiro-containing derivatives show antiparasitic activity against Trypanosoma brucei through inhibition of the trypanothione reductase enzyme. Authors: Turcano, L. / Battista, T. / De Haro, E.T. / Missineo, A. / Alli, C. / Paonessa, G. / Colotti, G. / Harper, S. / Fiorillo, A. / Ilari, A. / Bresciani, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.2 KB | Display | ![]() |
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PDB format | ![]() | 174.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 61 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wbaS S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55387.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q389T8, trypanothione-disulfide reductase |
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-Non-polymers , 5 types, 509 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/JWZ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/JWZ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-JWZ / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.54 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: SEEDING IN 0,1 M Hepes pH 6.8; 2.1 M Ammonium Sulphate |
-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: Jul 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 1.977→102.378 Å / Num. obs: 94907 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.078 / Net I/σ(I): 13.276 |
Reflection shell | Resolution: 1.977→2.012 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4693 / CC1/2: 0.788 / Rrim(I) all: 0.871 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WBA Resolution: 1.977→102.378 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.67 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.555 Å2
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Refinement step | Cycle: LAST / Resolution: 1.977→102.378 Å
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Refine LS restraints |
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