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Open data
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Basic information
Entry | Database: PDB / ID: 8pm8 | ||||||
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Title | V30M Transthyretin structure in complex with Tolcalpone | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Varejao, N. / Pinheiro, F. / Pallares, I. / Ventura, S. / Reverter, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: PITB: A high affinity transthyretin aggregation inhibitor with optimal pharmacokinetic properties. Authors: Pinheiro, F. / Varejao, N. / Sanchez-Morales, A. / Bezerra, F. / Navarro, S. / Velazquez-Campoy, A. / Busque, F. / Almeida, M.R. / Alibes, R. / Reverter, D. / Pallares, I. / Ventura, 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 | ![]() | 109.1 KB | Display | ![]() |
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PDB format | ![]() | 83.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8pm9C ![]() 8pmaC ![]() 8pmoC 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 13809.426 Da / Num. of mol.: 2 / Mutation: V30M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: 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: 2.1 Å3/Da / Density % sol: 41.45 % |
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Crystal grow![]() | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 0.2M CaCl2, 25% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.57→42.8 Å / Num. obs: 33424 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.99 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.57→1.6 Å / Num. unique obs: 1599 / CC1/2: 0.5 |
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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: 1.57→42.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.0047 Å / Origin y: 16.1099 Å / Origin z: 12.5933 Å
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Refinement TLS group | Selection details: all |