[English] 日本語
![](img/lk-miru.gif)
- PDB-7b02: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7b02 | ||||||
---|---|---|---|---|---|---|---|
Title | Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 4-Hydroxy-7-methyl-1,8-naphthyridine-3-carboxylic acid | ||||||
![]() | Thioredoxin glutathione reductase | ||||||
![]() | PROTEIN BINDING / fragment binding / redox enzyme / inhibitor / flavoreductase | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fata, F. / Silvestri, I. / Williams, D.L. / Angelucci, F. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 279.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 220.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 969.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 971.5 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 47.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zlbC ![]() 6zlpC ![]() 6zp3C ![]() 6zstC ![]() 7npxC ![]() 2v6oS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65061.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The structure is relative to the Sec597Cys mutant / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 8 types, 679 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SJN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SJN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-SJN / | #6: Chemical | ChemComp-K / | #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-NA / | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.18 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 3350, 0,2M potassium iodide, 0,1M Bis-TRIS, 5mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→39.93 Å / Num. obs: 135935 / % possible obs: 98.6 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.45→1.47 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5849 / CC1/2: 0.63 / % possible all: 86.1 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2V6O Resolution: 1.45→39.93 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.974 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 120.34 Å2 / Biso mean: 19.252 Å2 / Biso min: 0.5 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→39.93 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|