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Open data
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Basic information
Entry | Database: PDB / ID: 7pk3 | ||||||
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Title | Notum_ARUK3001185 | ||||||
![]() | Palmitoleoyl-protein carboxylesterase NOTUM | ||||||
![]() | SIGNALING PROTEIN / Notum Inhibitor | ||||||
Function / homology | ![]() [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / bone development / negative regulation of canonical Wnt signaling pathway ...[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / bone development / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endoplasmic reticulum lumen / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vecchia, L. / Hillier, J. / Zhao, Y. / Fish, P. / Jones, E.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design of a Potent, Selective, and Brain-Penetrant Inhibitor of Wnt-Deactivating Enzyme Notum by Optimization of a Crystallographic Fragment Hit. Authors: Willis, N.J. / Mahy, W. / Sipthorp, J. / Zhao, Y. / Woodward, H.L. / Atkinson, B.N. / Bayle, E.D. / Svensson, F. / Frew, S. / Jeganathan, F. / Monaghan, A. / Benvegnu, S. / Jolly, S. / ...Authors: Willis, N.J. / Mahy, W. / Sipthorp, J. / Zhao, Y. / Woodward, H.L. / Atkinson, B.N. / Bayle, E.D. / Svensson, F. / Frew, S. / Jeganathan, F. / Monaghan, A. / Benvegnu, S. / Jolly, S. / Vecchia, L. / Ruza, R.R. / Kjaer, S. / Howell, S. / Snijders, A.P. / Bictash, M. / Salinas, P.C. / Vincent, J.P. / Jones, E.Y. / Whiting, P. / Fish, P.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.2 KB | Display | ![]() |
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PDB format | ![]() | 125.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 911.5 KB | Display | ![]() |
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Full document | ![]() | 912.6 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pjrC ![]() 7pkvC ![]() 6r8pS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 43567.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 134 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/7T0.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/7T0.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-7T0 / | #5: Chemical | ChemComp-DMS / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.31 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate, pH4.2 |
-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: Apr 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→71.5 Å / Num. obs: 65798 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 1 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.41→1.43 Å / Num. unique obs: 3278 / CC1/2: 0.454 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6R8P Resolution: 1.41→52.82 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.08 / 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: 88.19 Å2 / Biso mean: 24.8021 Å2 / Biso min: 12.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.41→52.82 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23 / % reflection obs: 100 %
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