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- PDB-6zbq: Small-molecule inhibitors of the PDZ domain of Dishevelled protei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zbq | ||||||
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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 | ![]() : / frizzled binding / canonical Wnt signaling pathway / intracellular signal transduction / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roske, Y. / Heinemann, U. / Oschkinat, H. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97 KB | Display | ![]() |
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PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zbzC ![]() 6zc3C ![]() 6zc4C ![]() 6zc6C ![]() 6zc7C ![]() 6zc8C ![]() 2f0aS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30% PEG 8000, 0.2 M ammonium sulphate, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 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: 1.43→30.88 Å / Num. obs: 38358 / % possible obs: 100 % / Redundancy: 5.4 % / Rrim(I) all: 0.044 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.43→1.47 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2826 / Rrim(I) all: 0.0579 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2F0A Resolution: 1.43→30.88 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.628 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 112.55 Å2 / Biso mean: 25.244 Å2 / Biso min: 9.24 Å2
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Refinement step | Cycle: final / Resolution: 1.43→30.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.467 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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