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Open data
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Basic information
Entry | Database: PDB / ID: 5smj | |||||||||
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Title | Trypanothione reductase | |||||||||
![]() | N(1),N(8)-bis(glutathionyl)spermidine reductase | |||||||||
![]() | OXIDOREDUCTASE / Diamond I04-1 fragment screening / PanDDA / XChemExplorer | |||||||||
Function / homology | ![]() trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Fiorillo, A. / Ilari, A. | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Innovative Approach for a Classic Target: Fragment Screening on Trypanothione Reductase Reveals New Opportunities for Drug Design. Authors: Fiorillo, A. / Colotti, G. / Exertier, C. / Liuzzi, A. / Seghetti, F. / Salerno, A. / Caciolla, J. / Ilari, 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 | ![]() | 206.9 KB | Display | ![]() |
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PDB format | ![]() | 166.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 951.7 KB | Display | ![]() |
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Full document | ![]() | 956.9 KB | Display | |
Data in XML | ![]() | 39.8 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Group deposition
ID | G_1002198 (1 entries) |
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Title | PanDDA analysis group deposition of ground-state model |
Type | ground state |
Description | Trypanosoma brucei Trypanothione Reductase screened against the DSiP Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | ![]() 6rb5S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 53497.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A3L6KZJ1, trypanothione-disulfide reductase |
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-Non-polymers , 5 types, 547 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | #5: Chemical | ChemComp-BR / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD 22%, PEG 3350 14%, imidazole 40 mM pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 20, 2021 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91264 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.65→112.21 Å / Num. obs: 118791 / % possible obs: 98.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.4 | |||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6RB5 Resolution: 1.65→78.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.799 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 95.3 Å2 / Biso mean: 25.356 Å2 / Biso min: 10.31 Å2
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Refinement step | Cycle: final / Resolution: 1.65→78.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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