+Open data
-Basic information
Entry | Database: PDB / ID: 7b3f | ||||||
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Title | Notum S232A in complex with ARUK3003718 | ||||||
Components | Palmitoleoyl-protein carboxylesterase NOTUM | ||||||
Keywords | HYDROLASE / Notum Inhibitor | ||||||
Function / homology | Function and homology information [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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||
Authors | Zhao, Y. / Jone, E.Y. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structural Insights into Notum Covalent Inhibition. Authors: Zhao, Y. / Svensson, F. / Steadman, D. / Frew, S. / Monaghan, A. / Bictash, M. / Moreira, T. / Chalk, R. / Lu, W. / Fish, P.V. / Jones, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b3f.cif.gz | 162 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b3f.ent.gz | 126.3 KB | Display | PDB format |
PDBx/mmJSON format | 7b3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/7b3f ftp://data.pdbj.org/pub/pdb/validation_reports/b3/7b3f | HTTPS FTP |
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-Related structure data
Related structure data | 7argC 7b2vC 7b2yC 7b2zC 7b37C 7agrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 43551.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NOTUM, OK/SW-CL.30 / Production host: Homo sapiens (human) References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 99 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SRK / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: evaporation / pH: 4.2 / Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→47.78 Å / Num. obs: 68561 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 1 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.39→1.41 Å / Num. unique obs: 3349 / CC1/2: 0.462 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AGR Resolution: 1.39→47.78 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.53 / 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: 71.66 Å2 / Biso mean: 24.7805 Å2 / Biso min: 12.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.39→47.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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Refinement TLS params. | Method: refined / Origin x: 25.7169 Å / Origin y: 69.9285 Å / Origin z: 80.2548 Å
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Refinement TLS group |
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