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Yorodumi- PDB-3gs7: Human transthyretin (TTR) complexed with (E)-3-(2-methoxybenzylid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gs7 | ||||||
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Title | Human transthyretin (TTR) complexed with (E)-3-(2-methoxybenzylideneaminooxy)propanoic acid (inhibitor 13) | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE / transthyretin / inhibitor / amyloid / Amyloidosis / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Neuropathy / Polymorphism / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Mohamedmohaideen, N.N. / Palaninathan, S.K. / Orlandini, E. / Sacchettini, J.C. | ||||||
Citation | Journal: Plos One / Year: 2009 Title: Novel transthyretin amyloid fibril formation inhibitors: synthesis, biological evaluation, and X-ray structural analysis. Authors: Palaninathan, S.K. / Mohamedmohaideen, N.N. / Orlandini, E. / Ortore, G. / Nencetti, S. / Lapucci, A. / Rossello, A. / Freundlich, J.S. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gs7.cif.gz | 60.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gs7.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gs7_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 3gs7_full_validation.pdf.gz | 460.9 KB | Display | |
Data in XML | 3gs7_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 3gs7_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/3gs7 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/3gs7 | HTTPS FTP |
-Related structure data
Related structure data | 3glzC 3gs0C 3gs4C 1bmzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 13777.360 Da / Num. of mol.: 2 / Fragment: UNP residues 21 to 147 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: 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: 2.07 Å3/Da / Density % sol: 40.55 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystals of wt-TTR were obtained from 5-7 mg/mL protein solutions (in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, pH 7.0, 0.3 M ammonium sulfate) equilibrated against 2 M ammonium sulfate ...Details: Crystals of wt-TTR were obtained from 5-7 mg/mL protein solutions (in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, pH 7.0, 0.3 M ammonium sulfate) equilibrated against 2 M ammonium sulfate in hanging drops. All TTR:ligand complexes were prepared from crystals soaked with a ten fold molar excess of ligand for more than three weeks. , VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 16, 2008 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20.11 Å / Num. all: 21648 / Num. obs: 21648 / % possible obs: 98.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.847 Å / % possible all: 93.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1BMZ Resolution: 1.8→20.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.156 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.149 / 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: 40.261 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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