+Open data
-Basic information
Entry | Database: PDB / ID: 8wgs | ||||||
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Title | Crystal structure of V30M-TTR in complex with compound 4 | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Transthyretin / amyloidosis / inhibitor / benziodarone derivative | ||||||
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: 1.801 Å | ||||||
Authors | Yokoyama, T. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma. Authors: Mizuguchi, M. / Nakagawa, Y. / Yokoyama, T. / Okada, T. / Fujii, K. / Takahashi, K. / Luan, N.N.T. / Nabeshima, Y. / Kanamitsu, K. / Nakagawa, S. / Yamakawa, S. / Ueda, M. / Ando, Y. / Toyooka, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wgs.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wgs.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 8wgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/8wgs ftp://data.pdbj.org/pub/pdb/validation_reports/wg/8wgs | HTTPS FTP |
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-Related structure data
Related structure data | 8wgtC 8wguC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 17342.582 Da / Num. of mol.: 2 / Mutation: V30M 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 | Mass: 643.981 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H11I3O3 / Feature type: SUBJECT OF INVESTIGATION #3: 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: 1.7 Å3/Da / Density % sol: 27.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, sodium acetate, calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.7 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.97 Å / Num. obs: 22569 / % possible obs: 99.2 % / Redundancy: 8.4 % / CC1/2: 0.998 / Rpim(I) all: 0.028 / Rrim(I) all: 0.084 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.8→1.87 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2123 / CC1/2: 0.939 / Rpim(I) all: 0.209 / Rrim(I) all: 0.61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→38.691 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.801→38.691 Å
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Refine LS restraints |
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LS refinement shell |
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