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Yorodumi- PDB-6yuw: STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A PYRROLE-3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yuw | ||||||
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Title | STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A PYRROLE-3-CARBOXYLIC ACID FRAGMENT 454 | ||||||
Components | Palmitoleoyl-protein carboxylesterase NOTUM | ||||||
Keywords | HYDROLASE / Wnt / Wnt signalling / Frizzled / Fzd / Fragment screen / Notum | ||||||
Function / homology | Function and homology information [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development ...[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development / 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: 1.94 Å | ||||||
Authors | Ruza, R.R. / Hillier, J. / Jones, E.Y. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Screening of a Custom-Designed Acid Fragment Library Identifies 1-Phenylpyrroles and 1-Phenylpyrrolidines as Inhibitors of Notum Carboxylesterase Activity. Authors: Mahy, W. / Patel, M. / Steadman, D. / Woodward, H.L. / Atkinson, B.N. / Svensson, F. / Willis, N.J. / Flint, A. / Papatheodorou, D. / Zhao, Y. / Vecchia, L. / Ruza, R.R. / Hillier, J. / ...Authors: Mahy, W. / Patel, M. / Steadman, D. / Woodward, H.L. / Atkinson, B.N. / Svensson, F. / Willis, N.J. / Flint, A. / Papatheodorou, D. / Zhao, Y. / Vecchia, L. / Ruza, R.R. / Hillier, J. / Frew, S. / Monaghan, A. / Costa, A. / Bictash, M. / Walter, M.W. / Jones, E.Y. / Fish, P.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yuw.cif.gz | 176.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yuw.ent.gz | 131.2 KB | Display | PDB format |
PDBx/mmJSON format | 6yuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/6yuw ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yuw | HTTPS FTP |
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-Related structure data
Related structure data | 6yskC 6yuyC 6yv0C 6yv2C 6yv4C 6yxiC 4uz1S 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
#1: Protein | Mass: 43567.148 Da / Num. of mol.: 1 / Mutation: C330S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NOTUM, OK/SW-CL.30 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-PQZ / | #4: Sugar | ChemComp-NAG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1.4 M AMMONIUM SULPHATE, 0.1 M CITRIC ACID, PH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→78.4 Å / Num. obs: 39732 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 30.31 Å2 / CC1/2: 1 / Rrim(I) all: 0.097 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 12.8 % / Num. unique obs: 1935 / CC1/2: 0.8 / Rrim(I) all: 1.51 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UZ1 Resolution: 1.94→47.34 Å / SU ML: 0.2377 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.035 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 37.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→47.34 Å
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Refine LS restraints |
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LS refinement shell |
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