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- PDB-6zst: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zst | ||||||
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Title | Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 3-(3-methoxyquinoxalin-2-yl)propanoic 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 | ![]() | 143.6 KB | Display | ![]() |
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PDB format | ![]() | 108 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 980.8 KB | Display | ![]() |
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Full document | ![]() | 985.4 KB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zlbC ![]() 6zlpC ![]() 6zp3C ![]() 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 , 6 types, 474 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EY7.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EY7.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||||
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#3: Chemical | ChemComp-K / | ||||
#4: Chemical | ChemComp-PEG / | ||||
#5: Chemical | #6: Chemical | ChemComp-EY7 / | #7: 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: 3.05 Å3/Da / Density % sol: 59.67 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3350 20%, potassium iodide 0.2M, Bis-Tris 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 PILATUS 2M / Detector: PIXEL / Date: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.93 Å / Num. obs: 83411 / % possible obs: 97.7 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4363 / CC1/2: 0.8 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V6O Resolution: 1.7→39.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.841 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.089 / 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: 73.25 Å2 / Biso mean: 21.081 Å2 / Biso min: 10.16 Å2
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Refinement step | Cycle: final / Resolution: 1.7→39.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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