+Open data
-Basic information
Entry | Database: PDB / ID: 6tfb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Carbamazepine binds Frizzled8 | |||||||||
Components | Frizzled-8 | |||||||||
Keywords | ONCOPROTEIN / Wnt receptor Frizzled8 carbamazepine | |||||||||
Function / homology | Function and homology information Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / neuronal dense core vesicle / canonical Wnt signaling pathway / G protein-coupled receptor activity / PDZ domain binding ...Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / neuronal dense core vesicle / canonical Wnt signaling pathway / G protein-coupled receptor activity / PDZ domain binding / Wnt signaling pathway / cell-cell signaling / T cell differentiation in thymus / angiogenesis / positive regulation of protein phosphorylation / signaling receptor binding / ubiquitin protein ligase binding / Golgi apparatus / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Zhao, Y. / Jones, E.Y. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Antiepileptic Drug Carbamazepine Binds to a Novel Pocket on the Wnt Receptor Frizzled-8. Authors: Zhao, Y. / Ren, J. / Hillier, J. / Lu, W. / Jones, E.Y. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tfb.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tfb.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 6tfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tfb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6tfb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6tfb_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6tfb_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/6tfb ftp://data.pdbj.org/pub/pdb/validation_reports/tf/6tfb | HTTPS FTP |
-Related structure data
Related structure data | 6tfmC 1ijyS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15815.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fzd8 / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q61091 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.51 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, pH 5 1 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→52 Å / Num. obs: 30318 / % possible obs: 99.2 % / Redundancy: 11.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.68→1.71 Å / Mean I/σ(I) obs: 8.5 / Num. unique obs: 1412 / CC1/2: 0.84 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IJY Resolution: 1.68→50 Å / Cross valid method: THROUGHOUT
| ||||||||||||||||||
Displacement parameters | Biso max: 66.46 Å2 / Biso mean: 28 Å2 / Biso min: 2.54 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→50 Å
|