[English] 日本語
![](img/lk-miru.gif)
- PDB-6zc7: Small-molecule inhibitors of the PDZ domain of Dishevelled protei... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6zc7 | ||||||
---|---|---|---|---|---|---|---|
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 | ![]() | 96.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zbqC ![]() 6zbzC ![]() 6zc3C ![]() 6zc4C ![]() 6zc6C ![]() 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 | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.26 M sodium phosphate, 0.14 M potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 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: 1.48→34.55 Å / Num. obs: 40755 / % possible obs: 100 % / Redundancy: 8 % / Rrim(I) all: 0.0067 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.48→1.52 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3012 / Rrim(I) all: 0.0805 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2F0A Resolution: 1.48→34.55 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.172 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.057 / 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: 85.24 Å2 / Biso mean: 20.881 Å2 / Biso min: 10.43 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.48→34.55 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.48→1.518 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | T12: -0.0004 Å2 / T33: 0.009 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|