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- PDB-8p41: Crystal structure of glucocerebrosidase in complex with allosteri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p41 | ||||||
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Title | Crystal structure of glucocerebrosidase in complex with allosteric activator | ||||||
![]() | Glucosylceramidase![]() | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of protein lipidation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schulze, M.-S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Identification of ss-Glucocerebrosidase Activators for Glucosylceramide hydrolysis. Authors: Schulze, M.E.D. / Scholz, D. / Jnoff, E. / Hall, A. / Melin, J. / Sands, Z.A. / Rodriguez, E. / Andre, V.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.4 KB | Display | ![]() |
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PDB format | ![]() | 175.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8p3eC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 55640.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P04062, ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 3 types, 471 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / ![]() #5: Chemical | Mass: 471.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H12ClF6NO3S / Feature type: SUBJECT OF INVESTIGATION #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.77 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion / Details: 2 M (NH4)2SO4, 0.1 M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.83→47.59 Å / Num. obs: 230144 / % possible obs: 97 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.83→1.88 Å / Rmerge(I) obs: 0.666 / Num. unique obs: 8561 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→46.97 Å
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Refine LS restraints |
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LS refinement shell |
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