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Yorodumi- PDB-6ti9: Human transthyretin (TTR) complexed with (E)-3-(((3,5-dibromo-2-h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ti9 | ||||||
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Title | Human transthyretin (TTR) complexed with (E)-3-(((3,5-dibromo-2-hydroxybenzylidene)amino)oxy)propanoic acid. | ||||||
Components | Transthyretin | ||||||
Keywords | PROTEIN TRANSPORT / Transthyretin / TTR / inhibitor / complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Ciccone, L. / Nencetti, S. / Orlandini, E. / Rossello, A. / Legrand, P. / Shepard, W. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2020 Title: Monoaryl derivatives as transthyretin fibril formation inhibitors: Design, synthesis, biological evaluation and structural analysis. Authors: Ciccone, L. / Nencetti, S. / Tonali, N. / Fruchart-Gaillard, C. / Shepard, W. / Nuti, E. / Camodeca, C. / Rossello, A. / Orlandini, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ti9.cif.gz | 157.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ti9.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ti9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ti9_validation.pdf.gz | 996.9 KB | Display | wwPDB validaton report |
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Full document | 6ti9_full_validation.pdf.gz | 999.7 KB | Display | |
Data in XML | 6ti9_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 6ti9_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/6ti9 ftp://data.pdbj.org/pub/pdb/validation_reports/ti/6ti9 | HTTPS FTP |
-Related structure data
Related structure data | 6tjnC 5e23S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 13834.413 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 4.93 mg/mL, Tris pH 8.0, 150mM NaCl. Precipitant: 24% PEG 600, 0.2M imidazole malate pH 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.919491 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919491 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 42796 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 1 / Net I/σ(I): 1.96 |
Reflection shell | Resolution: 1.45→1.46 Å / Num. unique obs: 60556 / CC1/2: 0.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+23 / Resolution: 1.45→24.584 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.41 / Stereochemistry target values: MLHL
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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 max: 125.94 Å2 / Biso mean: 27.1146 Å2 / Biso min: 13.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→24.584 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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