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Open data
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Basic information
Entry | Database: PDB / ID: 8w45 | ||||||
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Title | X-ray crystal structure of V30M-TTR in complex with pinostilbene | ||||||
![]() | Transthyretin![]() | ||||||
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Function / homology | ![]() Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yokoyama, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Resveratrol Derivatives Inhibit Transthyretin Fibrillization: Structural Insights into the Interactions between Resveratrol Derivatives and Transthyretin. Authors: Yokoyama, T. / Kusaka, K. / Mizuguchi, M. / Nabeshima, Y. / Fujiwara, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.1 KB | Display | ![]() |
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PDB format | ![]() | 136.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8w42C ![]() 8w43C ![]() 8w44C ![]() 8w46C ![]() 8w47C ![]() 8w48C C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 17342.582 Da / Num. of mol.: 2 / Mutation: V30M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #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: 1.67 Å3/Da / Density % sol: 26.29 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Disodium malonate, 0.1M NaOAc pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.1→35.09 Å / Num. obs: 91660 / % possible obs: 96.62 % / Redundancy: 6.81 % / CC1/2: 0.999 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.1→1.14 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7218 / CC1/2: 0.846 / Rpim(I) all: 0.255 / Rrim(I) all: 0.554 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→31.614 Å
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Refine LS restraints |
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LS refinement shell |
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