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- PDB-1dvz: CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH O-TRIFLU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dvz | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH O-TRIFLUOROMETHYLPHENYL ANTHRANILIC ACID | ||||||
![]() | TRANSTHYRETIN![]() | ||||||
![]() | HORMONE/GROWTH FACTOR / THYROXINE TRANSPORT / ![]() | ||||||
Function / homology | ![]() Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Klabunde, T. / Petrassi, H.M. / Oza, V.B. / Kelly, J.W. / Sacchettini, J.C. | ||||||
![]() | ![]() Title: Rational design of potent human transthyretin amyloid disease inhibitors. Authors: Klabunde, T. / Petrassi, H.M. / Oza, V.B. / Raman, P. / Kelly, J.W. / Sacchettini, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1dvqC ![]() 1dvsC ![]() 1dvtC ![]() 1dvuC ![]() 1dvxC ![]() 1dvyC C: citing same article ( |
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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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Details | The biological assembly is a tetramer constructed from the homodimer (chain A and B) and a symmetry mate by the two-fold. |
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Components
#1: Protein | ![]() Mass: 13420.968 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-OFL / | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: potassium chloride, potassium phosphate, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 2, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→10 Å / Num. all: 22485 / Num. obs: 22485 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.58 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.373 / % possible all: 96.9 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 102879 |
Reflection shell | *PLUS % possible obs: 96.9 % |
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Processing
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Refinement | Resolution: 1.9→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: The structure contains two OFLU molecules that bind in each of two independent binding sites of the tetramer. Since the binding is along the 2-fold crystallographic axis, an occupancy of 0.5 ...Details: The structure contains two OFLU molecules that bind in each of two independent binding sites of the tetramer. Since the binding is along the 2-fold crystallographic axis, an occupancy of 0.5 corresponds to saturation of each of the binding sites. Binding of OFLU in two symmetry-related binding modes induces alternate side chain conformations for the protein residues Lys15 and Leu17.
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.192 / Rfactor Rfree![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |