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- PDB-6d0w: Structure of human transthyretin complex with analgesic inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d0w | ||||||
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Title | Structure of human transthyretin complex with analgesic inhibitor | ||||||
![]() | Transthyretin | ||||||
![]() | Protein Transport/Protein Transport Inhibitor / transthyretin transport protein inhibitor complex / PROTEIN TRANSPORT / Protein Transport-Protein Transport Inhibitor 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 | ![]() ![]() ![]() | ||||||
![]() | Cody, V. | ||||||
![]() | ![]() Title: Structural Analysis of Human Transthyretin Analgesic Inhibitor Complex Authors: Cody, V. / Richardson, 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 | ![]() | 62.8 KB | Display | ![]() |
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PDB format | ![]() | 43.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2roxS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13776.376 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 44.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M MES, pH 5.5, PEG 4K, 150 mM AmSO4 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 3, 2013 |
Radiation | Monochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→39.1 Å / Num. obs: 35885 / % possible obs: 96 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.014 / Rsym value: 0.043 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.53→1.61 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4266 / % possible all: 79.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ROX Resolution: 1.7→36.43 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.801 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.59 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→36.43 Å
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Refine LS restraints |
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