[English] 日本語
Yorodumi- PDB-6r8q: STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A BENZOTRIAZ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r8q | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A BENZOTRIAZOLE FRAGMENT | |||||||||
Components | Palmitoleoyl-protein carboxylesterase NOTUM | |||||||||
Keywords | HYDROLASE / Wnt signalling / NOTUM Inhibitor / Crystallographic Fragment Screen | |||||||||
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: 1.5 Å | |||||||||
Authors | Ruza, R.R. / Vecchia, L. / Jones, E.Y. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: Medchemcomm / Year: 2019 Title: Discovery of 2-phenoxyacetamides as inhibitors of the Wnt-depalmitoleating enzyme NOTUM from an X-ray fragment screen. Authors: Atkinson, B.N. / Steadman, D. / Zhao, Y. / Sipthorp, J. / Vecchia, L. / Ruza, R.R. / Jeganathan, F. / Lines, G. / Frew, S. / Monaghan, A. / Kjær, S. / Bictash, M. / Jones, E.Y. / Fish, P.V. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6r8q.cif.gz | 173.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6r8q.ent.gz | 133.8 KB | Display | PDB format |
PDBx/mmJSON format | 6r8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/6r8q ftp://data.pdbj.org/pub/pdb/validation_reports/r8/6r8q | HTTPS FTP |
---|
-Related structure data
Related structure data | 6r8pC 6r8rC 4uz1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#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 |
---|---|
#2: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 216 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-JV5 / ~{ | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.04 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→52.69 Å / Num. obs: 54581 / % possible obs: 99.91 % / Redundancy: 12.53 % / Biso Wilson estimate: 16.42 Å2 / CC1/2: 0.9978 / Net I/σ(I): 9.62 |
Reflection shell | Resolution: 1.5→1.52 Å / Num. unique obs: 2568 / CC1/2: 0.6098 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UZ1 Resolution: 1.5→52.689 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 19.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.88 Å2 / Biso mean: 21.8566 Å2 / Biso min: 8.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→52.689 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
|