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Open data
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Basic information
Entry | Database: PDB / ID: 8bta | |||||||||
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Title | Notum Inhibitor ARUK3004308 | |||||||||
![]() | Palmitoleoyl-protein carboxylesterase NOTUM | |||||||||
![]() | HYDROLASE / Inhibitor Notum | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Zhao, Y. / Jones, E.Y. / Fish, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Designed switch from covalent to non-covalent inhibitors of carboxylesterase Notum activity. Authors: Atkinson, B.N. / Willis, N.J. / Zhao, Y. / Patel, C. / Frew, S. / Costelloe, K. / Magno, L. / Svensson, F. / Jones, E.Y. / 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 | ![]() | 160.2 KB | Display | ![]() |
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PDB format | ![]() | 127.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 854 KB | Display | ![]() |
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Full document | ![]() | 856.8 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bspC ![]() 8bsqC ![]() 8bsrC ![]() 8bszC ![]() 8bt0C ![]() 8bt2C ![]() 8bt5C ![]() 8bt7C ![]() 8bt8C ![]() 8btcC ![]() 8bteC ![]() 8bthC ![]() 8btiC 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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1 |
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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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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 104 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/RC6.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/RC6.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-DMS / #5: Chemical | #6: Chemical | ChemComp-RC6 / | #7: 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: 1.94 Å3/Da / Density % sol: 36.56 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.2 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 EIGER2 XE 16M / Detector: PIXEL / Date: Jul 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→53.08 Å / Num. obs: 76751 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.34→1.36 Å / Num. unique obs: 3785 / CC1/2: 0.354 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→53.08 Å
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Refine LS restraints |
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LS refinement shell |
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