+Open data
-Basic information
Entry | Database: PDB / ID: 7erj | ||||||
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Title | Crystal structure of V30M-TTR in complex with dichlorophen | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Amyloidosis / 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: 1.892 Å | ||||||
Authors | Yokoyama, T. / Kashihara, M. / Mizuguchi, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Repositioning of the Anthelmintic Drugs Bithionol and Triclabendazole as Transthyretin Amyloidogenesis Inhibitors. Authors: Yokoyama, T. / Kashihara, M. / Mizuguchi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7erj.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7erj.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 7erj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7erj_validation.pdf.gz | 1005.8 KB | Display | wwPDB validaton report |
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Full document | 7erj_full_validation.pdf.gz | 1006.7 KB | Display | |
Data in XML | 7erj_validation.xml.gz | 12 KB | Display | |
Data in CIF | 7erj_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/7erj ftp://data.pdbj.org/pub/pdb/validation_reports/er/7erj | HTTPS FTP |
-Related structure data
Related structure data | 7erhC 7eriC 7erkC 4pweS 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: 17342.582 Da / Num. of mol.: 2 / Mutation: V50M 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-CA / | #4: 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: 1.71 Å3/Da / Density % sol: 28.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, CaCl2, NaOAc, dichlorophen |
-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: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→42.93 Å / Num. obs: 19423 / % possible obs: 98.8 % / Redundancy: 5.1 % / CC1/2: 0.994 / Rpim(I) all: 0.04 / Rrim(I) all: 0.089 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.89→1.96 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1741 / CC1/2: 0.827 / Rpim(I) all: 0.31 / Rrim(I) all: 0.727 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PWE Resolution: 1.892→42.93 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.26 / 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: 1.892→42.93 Å
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Refine LS restraints |
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LS refinement shell |
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