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- PDB-7acu: Crystal structure of human transthyretin in complex with Benzbromarone -
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Open data
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Basic information
Entry | Database: PDB / ID: 7acu | ||||||
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Title | Crystal structure of human transthyretin in complex with Benzbromarone | ||||||
![]() | Transthyretin | ||||||
![]() | TRANSPORT PROTEIN / transthyretin / TTR / benzbromarone / complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Leite, J.P. / Gales, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Repurposing Benzbromarone for Familial Amyloid Polyneuropathy: A New Transthyretin Tetramer Stabilizer. Authors: Cotrina, E.Y. / Oliveira, A. / Leite, J.P. / Llop, J. / Gales, L. / Quintana, J. / Cardoso, I. / Arsequell, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.9 KB | Display | ![]() |
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PDB format | ![]() | 83.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1y1dS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
NCS ensembles :
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Components
#1: Protein | Mass: 12606.103 Da / Num. of mol.: 2 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: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.2 M acetate buffer pH 4.8, 2.2 M ammonium sulfate, 7% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→64.39 Å / Num. obs: 52367 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 20.13 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.35→64.39 Å / Rmerge(I) obs: 0.071 / Num. unique obs: 321843 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Y1D Resolution: 1.541→35.47 Å / SU ML: 0.1528 / Cross valid method: FREE R-VALUE / σ(F): 2.2 / Phase error: 19.3296 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 30.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.541→35.47 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: -22.1749506108 Å / Origin y: 55.2034672258 Å / Origin z: 48.1791623173 Å
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Refinement TLS group | Selection details: all |