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- PDB-6zp3: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zp3 | ||||||
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Title | Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 2-Methylindole-3-acetic acid | ||||||
![]() | Thioredoxin glutathione reductase | ||||||
![]() | PROTEIN BINDING / fragment binding / redox enzyme / inhibitor | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / cell redox homeostasis / flavin adenine dinucleotide binding / electron transfer activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fata, F. / Silvestri, I. / Williams, D.L. / Angelucci, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments. Authors: Fata, F. / Silvestri, I. / Ardini, M. / Ippoliti, R. / Di Leandro, L. / Demitri, N. / Polentarutti, M. / Di Matteo, A. / Lyu, H. / Thatcher, G.R.J. / Petukhov, P.A. / Williams, D.L. / Angelucci, 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 | ![]() | 353.6 KB | Display | ![]() |
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PDB format | ![]() | 288.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zlbC ![]() 6zlpC ![]() 6zstC ![]() 7b02C ![]() 7npxC ![]() 2v6oS 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65108.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: G4V8J4, thioredoxin-disulfide reductase |
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-Non-polymers , 10 types, 355 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/QN5.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/QN5.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / |
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#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-PG4 / |
#5: Chemical | ChemComp-DMS / |
#6: Chemical | ChemComp-QN5 / |
#7: Chemical | ChemComp-CA / |
#8: Chemical | ChemComp-PEG / |
#9: Chemical | ChemComp-DTT / |
#10: Chemical | ChemComp-PGE / |
#11: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.18 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 3350 20%, potassium iodide 0.2, BisTris 0.1M, DTT 5mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39.684 Å / Num. obs: 70295 / % possible obs: 98.9 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4221 / CC1/2: 0.769 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V6O Resolution: 1.8→39.684 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.09 Å2 / Biso mean: 34.4444 Å2 / Biso min: 11.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→39.684 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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