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- PDB-7ytv: Crystal structure of Aspergillus fumigatus Thioredoxin reductase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ytv | ||||||
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Title | Crystal structure of Aspergillus fumigatus Thioredoxin reductase in complex with auranofin | ||||||
![]() | Thioredoxin reductase | ||||||
![]() | OXIDOREDUCTASE / Thioredoxin reductase / reductase / auranofin | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: In vitro antifungal and antibiofilm activities of auranofin against itraconazole-resistant Aspergillus fumigatus. Authors: Chen, P. / Yang, J. / Jin, Y. / Lu, C. / Feng, Z. / Gao, F. / Chen, Y. / Wang, F. / Shang, Z. / Lin, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.3 KB | Display | ![]() |
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PDB format | ![]() | 105 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bpyS 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
#1: Protein | Mass: 39862.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A229Y1X4, thioredoxin-disulfide reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.72 Å3/Da / Density % sol: 78.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium phosphate monobasic monohydrate, 20% (w/v) PEG 3350 |
-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: Jan 22, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.866→132.34 Å / Num. obs: 17428 / % possible obs: 99.8 % / Redundancy: 19.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.263 / Rpim(I) all: 0.062 / Rrim(I) all: 0.27 / Net I/σ(I): 10.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BPY Resolution: 3.866→59.432 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.53 / 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: 284.59 Å2 / Biso mean: 143.1834 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.866→59.432 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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