+Open data
-Basic information
Entry | Database: PDB / ID: 7b3p | ||||||
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Title | Notum complex with ARUK3003775 | ||||||
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 / bone development / Post-translational protein phosphorylation / 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 / bone development / Post-translational protein phosphorylation / 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: 1.28 Å | ||||||
Authors | Zhao, Y. / Jones, E.Y. / Fish, P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2022 Title: Virtual Screening Directly Identifies New Fragment-Sized Inhibitors of Carboxylesterase Notum with Nanomolar Activity. Authors: Steadman, D. / Atkinson, B.N. / Zhao, Y. / Willis, N.J. / Frew, S. / Monaghan, A. / Patel, C. / Armstrong, E. / Costelloe, K. / Magno, L. / Bictash, M. / Jones, E.Y. / Fish, P.V. / Svensson, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b3p.cif.gz | 156.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b3p.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 7b3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/7b3p ftp://data.pdbj.org/pub/pdb/validation_reports/b3/7b3p | HTTPS FTP |
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-Related structure data
Related structure data | 7b3gC 7b3hC 7b3iC 7b3xC 7b45C 7b50C 7argS 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 , 1 types, 1 molecules A
#1: Protein | Mass: 43567.148 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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-Non-polymers , 5 types, 124 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SUQ / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-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: 36.42 % |
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Crystal grow | Temperature: 296 K / Method: evaporation / 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: 1.28→53.25 Å / Num. obs: 87713 / % possible obs: 100 % / Redundancy: 26.1 % / CC1/2: 1 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.28→1.3 Å / Num. unique obs: 4329 / CC1/2: 0.813 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ARG Resolution: 1.28→46.04 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.88 / 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: 83.4 Å2 / Biso mean: 22.2427 Å2 / Biso min: 12.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.28→46.04 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 24.902 Å / Origin y: 71.5952 Å / Origin z: 80.8036 Å
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Refinement TLS group |
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