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- PDB-5aks: Transthyretin binding heterogeneity and anti-amyloidogenic activi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5aks | ||||||
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Title | Transthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites: resveratrol-3-O- glucuronide | ||||||
![]() | TRANSTHYRETIN | ||||||
![]() | TRANSPORT PROTEIN / AMYLOID / FIBRILLOGENESIS / FIBRILLOGENESIS INHIBITORS / POLYPHENOLS / POLYPHENOL METABOLITES / TRANSTHYRETIN / NEGATIVE COOPERATIVITY | ||||||
Function / homology | ![]() Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Florio, P. / Foll, C. / Cianci, M. / Del Rio, D. / Zanotti, G. / Berni, R. | ||||||
![]() | ![]() Title: Transthyretin Binding Heterogeneity and Anti-Amyloidogenic Activity of Natural Polyphenols and Their Metabolites Authors: Florio, P. / Folli, C. / Cianci, M. / Del Rio, D. / Zanotti, G. / Berni, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.1 KB | Display | ![]() |
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PDB format | ![]() | 58.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 907.6 KB | Display | ![]() |
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Full document | ![]() | 919.8 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5aktC ![]() 5akvC ![]() 5al0C ![]() 5al8C ![]() 5cr1C ![]() 1f41S C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 13777.360 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.76 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN ...Details: CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN 20 MM SODIUM PHOSPHATE, PH 7, WAS INCUBATED WITH A FOUR-FOLD MOLAR EXCESS OF LIGANDS SOLUBILIZED IN DMSO. DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF THE SOLUTION CONTAINING LIGAND-TTR COMPLEXES AND OF THE RESERVOIR/PRECIPITANT SOLUTION (2.2 M AMMONIUM SULPHATE, 0.1 M KCL, 0.03 M SODIUM PHOSPHATE, PH 7.0). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2013 / Details: KB MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.967 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→63.79 Å / Num. obs: 61920 / % possible obs: 95.1 % / Observed criterion σ(I): 3.5 / Redundancy: 6.7 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 3.5 / % possible all: 80.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F41 Resolution: 1.25→63.793 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 20.35 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→63.793 Å
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Refine LS restraints |
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LS refinement shell |
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