[English] 日本語
![](img/lk-miru.gif)
- PDB-6zc3: Small-molecule inhibitors of the PDZ domain of Dishevelled protei... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6zc3 | ||||||
---|---|---|---|---|---|---|---|
Title | Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling | ||||||
![]() | Dishevelled, dsh homolog 3 (Drosophila), isoform CRA_b | ||||||
![]() | PEPTIDE BINDING PROTEIN / PDZ / DVL / Inhibitors / Wnt / signalling | ||||||
Function / homology | ![]() planar cell polarity pathway involved in neural tube closure / frizzled binding / canonical Wnt signaling pathway / intracellular signal transduction / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roske, Y. / Heinemann, U. / Oschkinat, H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling Authors: Roske, Y. / Heinemann, U. / Oschkinat, H. / Kamdem, N. / Kovalskyy, D. / Platonov, M.O. / Balinskyi, O.M. / Kreuchwig, A. / Saupe, J. / Fang, L. / Diehl, A. / Schmieder, P. / Krause, G. / ...Authors: Roske, Y. / Heinemann, U. / Oschkinat, H. / Kamdem, N. / Kovalskyy, D. / Platonov, M.O. / Balinskyi, O.M. / Kreuchwig, A. / Saupe, J. / Fang, L. / Diehl, A. / Schmieder, P. / Krause, G. / Rademann, J. / Birchmeier, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 94.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 72.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zbqC ![]() 6zbzC ![]() 6zc4C ![]() 6zc6C ![]() 6zc7C ![]() 6zc8C ![]() 2f0aS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 10199.681 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.55 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.2 M ammonium sulphate, 0.1 M citric acid pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→34.84 Å / Num. obs: 29202 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rrim(I) all: 0.0055 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.67→1.71 Å / Num. unique obs: 2161 / Rrim(I) all: 0.0774 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2F0A Resolution: 1.67→34.84 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.082 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.36 Å2 / Biso mean: 30.414 Å2 / Biso min: 16.55 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.67→34.84 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.67→1.713 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|