+Open data
-Basic information
Entry | Database: PDB / ID: 2f8i | ||||||
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Title | Human transthyretin (TTR) complexed with Benzoxazole | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE/GROWTH FACTOR / TTR / AMYLOID / TRANSTHYRETIN / HORMONE-GROWTH FACTOR 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: 1.541 Å | ||||||
Authors | Palaninathan, S.K. / Mohamedmohaideen, N.N. / Sacchettini, J.C. / Kelly, J.W. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2003 Title: Benzoxazoles as transthyretin amyloid fibril inhibitors: synthesis, evaluation, and mechanism of action Authors: Razavi, H. / Palaninathan, S.K. / Powers, E.T. / Wiseman, R.L. / Purkey, H.E. / Mohamedmohaideen, N.N. / Deechongkit, S. / Chiang, K.P. / Dendle, M.T. / Sacchettini, J.C. / Kelly, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f8i.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f8i.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 2f8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/2f8i ftp://data.pdbj.org/pub/pdb/validation_reports/f8/2f8i | HTTPS FTP |
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-Related structure data
Related structure data | 1bmzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13777.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: PHNTR, PKNTR / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 42.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 MM EDTA, 100 mM KCL, 10 MM SODIUM R 0.35 M AMMONIUM SULFATE - CRYSTALS WERE SOAKED WITH THE INHIBITOR, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2002 |
Radiation | Monochromator: Bent Ge monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→35.36 Å / Num. all: 30705 / Num. obs: 30705 / % possible obs: 86 % / Observed criterion σ(I): -1 / Rsym value: 0.05 |
Reflection shell | Resolution: 1.54→1.58 Å / Rsym value: 0.39 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BMZ Resolution: 1.541→35.36 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.685 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.487 Å2
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Refinement step | Cycle: LAST / Resolution: 1.541→35.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.541→1.581 Å / Total num. of bins used: 20
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