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Yorodumi- PDB-6y6t: Mouse Galactocerebrosidase complexed with galacto-noeurostegine G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y6t | ||||||
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Title | Mouse Galactocerebrosidase complexed with galacto-noeurostegine GNS at pH 4.6 | ||||||
Components | GalactocerebrosidaseGalactosylceramidase | ||||||
Keywords | HYDROLASE / Inhibitor | ||||||
Function / homology | Function and homology information Glycosphingolipid catabolism / galactosylceramide catabolic process / galactosylceramidase / galactosylceramidase activity / myelination / lysosome / mitochondrion Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Deane, J.E. / McLoughlin, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 Title: The Bicyclic Form of galacto -Noeurostegine Is a Potent Inhibitor of beta-Galactocerebrosidase. Authors: Viuff, A. / Salamone, S. / McLoughlin, J. / Deane, J.E. / Jensen, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y6t.cif.gz | 334.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y6t.ent.gz | 225.8 KB | Display | PDB format |
PDBx/mmJSON format | 6y6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/6y6t ftp://data.pdbj.org/pub/pdb/validation_reports/y6/6y6t | HTTPS FTP |
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-Related structure data
Related structure data | 6y6sC 3zr5S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74596.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Galc / Production host: Homo sapiens (human) / References: UniProt: P54818, galactosylceramidase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 250 molecules
#3: Chemical | ChemComp-ODW / ( |
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#5: Chemical | ChemComp-CA / |
#6: Chemical | ChemComp-NI / |
#7: Water | ChemComp-HOH / |
-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: 3.17 Å3/Da / Density % sol: 61.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate (pH 6.8), and 34% wt/vol polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→41.98 Å / Num. obs: 44274 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 47.76 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.25→2.29 Å / Num. unique obs: 2225 / CC1/2: 0.524 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3zr5 Resolution: 2.25→41.98 Å / SU ML: 0.3031 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.7331
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→41.98 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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