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Yorodumi- PDB-6suh: Crystal structure of human transthyretin in complex with 3-O-meth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6suh | ||||||
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Title | Crystal structure of human transthyretin in complex with 3-O-methyltolcapone, a tolcapone analogue | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Amyloidosis / tetramer / binding protein | ||||||
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: 1.26 Å | ||||||
Authors | Loconte, V. / Cianci, M. / Menozzi, I. / Sbravati, D. / Sansone, F. / Casnati, A. / Berni, R. | ||||||
Citation | Journal: Bioorg.Chem. / Year: 2020 Title: Interactions of tolcapone analogues as stabilizers of the amyloidogenic protein transthyretin. Authors: Loconte, V. / Cianci, M. / Menozzi, I. / Sbravati, D. / Sansone, F. / Casnati, A. / Berni, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6suh.cif.gz | 158.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6suh.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 6suh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6suh_validation.pdf.gz | 985.3 KB | Display | wwPDB validaton report |
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Full document | 6suh_full_validation.pdf.gz | 988.9 KB | Display | |
Data in XML | 6suh_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 6suh_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/6suh ftp://data.pdbj.org/pub/pdb/validation_reports/su/6suh | HTTPS FTP |
-Related structure data
Related structure data | 6sugC 5aksS 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: 15904.984 Da / Num. of mol.: 2 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: 1.88 Å3/Da / Density % sol: 33.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.2 M ammonium sulfate, 0.1M KCl, 30 mM sodium phosphate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→42.91 Å / Num. obs: 64681 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 11 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.058 / Rsym value: 0.086 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.26→1.28 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3086 / CC1/2: 0.485 / Rpim(I) all: 0.96 / Rsym value: 1.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AKS Resolution: 1.26→42.731 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.48 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.38 Å2 / Biso mean: 21.3909 Å2 / Biso min: 8.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.26→42.731 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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