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Open data
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Basic information
Entry | Database: PDB / ID: 8bsr | ||||||
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Title | Notum Inhibitor ARUK3006562 | ||||||
![]() | Palmitoleoyl-protein carboxylesterase NOTUM | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 160.7 KB | Display | ![]() |
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PDB format | ![]() | 126.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bspC ![]() 8bsqC ![]() 8bszC ![]() 8bt0C ![]() 8bt2C ![]() 8bt5C ![]() 8bt7C ![]() 8bt8C ![]() 8btaC ![]() 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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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 , 5 types, 127 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/RCU.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/RCU.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-DMS / | ![]() #5: Chemical | ChemComp-RCU / | #6: Chemical | ![]() #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: 36.64 % |
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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: Nov 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.45→47.69 Å / Num. obs: 60890 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 1 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.45→1.47 Å / Num. unique obs: 2956 / CC1/2: 0.68 |
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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: 1.45→46.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 25.3919 Å / Origin y: -1.3248 Å / Origin z: 2.2828 Å
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Refinement TLS group | Selection details: all |