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Open data
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Basic information
Entry | Database: PDB / ID: 7bm7 | ||||||
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Title | Notum fragment 5e | ||||||
![]() | Palmitoleoyl-protein carboxylesterase NOTUM | ||||||
![]() | HYDROLASE / 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 | ![]() ![]() ![]() | ||||||
![]() | Zhao, Y. / Jones, E.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Notum Inhibitor Authors: Zhao, Y. / Jones, E.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.9 KB | Display | ![]() |
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PDB format | ![]() | 62.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747.3 KB | Display | ![]() |
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Full document | ![]() | 748.8 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bltC ![]() 7bluC ![]() 7blwC ![]() 7bm1C ![]() 7bm3C ![]() 7bn5C ![]() 7bn8C ![]() 7bnbC ![]() 7bncC ![]() 7bneC ![]() 7bnfC ![]() 7bnjC ![]() 7bo2C ![]() 7bo5C ![]() 4uz1S 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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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, 73 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/U3Q.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/U3Q.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-U3Q / | #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: 1.92 Å3/Da / Density % sol: 36.01 % |
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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 S 6M / Detector: PIXEL / Date: Sep 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→52.9 Å / Num. obs: 28318 / % possible obs: 99.6 % / Redundancy: 17.4 % / CC1/2: 0.999 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.87→1.9 Å / Num. unique obs: 1313 / CC1/2: 0.573 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4uz1 Resolution: 1.87→52.9 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.75 / 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: 90.11 Å2 / Biso mean: 32.8788 Å2 / Biso min: 9.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.87→52.9 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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