+Open data
-Basic information
Entry | Database: PDB / ID: 8pm8 | ||||||
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Title | V30M Transthyretin structure in complex with Tolcalpone | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Aggregation / Inhibitor / Amyloid | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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: 1.57 Å | ||||||
Authors | Varejao, N. / Pinheiro, F. / Pallares, I. / Ventura, S. / Reverter, D. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2023 Title: PITB: A high affinity transthyretin aggregation inhibitor with optimal pharmacokinetic properties. Authors: Pinheiro, F. / Varejao, N. / Sanchez-Morales, A. / Bezerra, F. / Navarro, S. / Velazquez-Campoy, A. / Busque, F. / Almeida, M.R. / Alibes, R. / Reverter, D. / Pallares, I. / Ventura, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pm8.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pm8.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 8pm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/8pm8 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/8pm8 | HTTPS FTP |
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-Related structure data
Related structure data | 8pm9C 8pmaC 8pmoC 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: 13809.426 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 | #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: 2.1 Å3/Da / Density % sol: 41.45 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 0.2M CaCl2, 25% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979339 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979339 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→42.8 Å / Num. obs: 33424 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.99 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.57→1.6 Å / Num. unique obs: 1599 / CC1/2: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→42.5 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.73 / 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: 1.57→42.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.0047 Å / Origin y: 16.1099 Å / Origin z: 12.5933 Å
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Refinement TLS group | Selection details: all |