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Open data
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Basic information
Entry | Database: PDB / ID: 9fb2 | ||||||
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Title | Gcase in complex with small molecule inhibitor 1 | ||||||
![]() | Lysosomal acid glucosylceramidase | ||||||
![]() | LIPID BINDING PROTEIN / Glycosidase / cholesterol metabolism / steroid metabolism / glycosyl transferase | ||||||
Function / homology | ![]() positive regulation of protein lipidation / steryl-beta-glucosidase activity / beta-glucoside catabolic process / positive regulation of neuronal action potential / cerebellar Purkinje cell layer formation / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / lymphocyte migration ...positive regulation of protein lipidation / steryl-beta-glucosidase activity / beta-glucoside catabolic process / positive regulation of neuronal action potential / cerebellar Purkinje cell layer formation / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / lymphocyte migration / glucosylceramidase / scavenger receptor binding / glucosylceramide catabolic process / regulation of lysosomal protein catabolic process / autophagosome organization / glucosylceramidase activity / microglial cell proliferation / sphingosine biosynthetic process / glucosyltransferase activity / regulation of TOR signaling / ceramide biosynthetic process / lipid storage / microglia differentiation / response to thyroid hormone / Glycosphingolipid catabolism / pyramidal neuron differentiation / lipid glycosylation / brain morphogenesis / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / response to pH / positive regulation of protein-containing complex disassembly / motor behavior / neuromuscular process / Transferases; Glycosyltransferases; Hexosyltransferases / hematopoietic stem cell proliferation / lysosome organization / response to testosterone / response to dexamethasone / Association of TriC/CCT with target proteins during biosynthesis / antigen processing and presentation / negative regulation of interleukin-6 production / homeostasis of number of cells / regulation of macroautophagy / establishment of skin barrier / negative regulation of protein-containing complex assembly / positive regulation of protein dephosphorylation / cell maturation / cellular response to starvation / respiratory electron transport chain / cholesterol metabolic process / lysosomal lumen / negative regulation of MAP kinase activity / determination of adult lifespan / trans-Golgi network / autophagy / negative regulation of inflammatory response / response to estrogen / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to tumor necrosis factor / T cell differentiation in thymus / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / negative regulation of neuron apoptotic process / lysosome / lysosomal membrane / signaling receptor binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tisi, D. / Cleasby, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Fragment-Based Discovery of a Series of Allosteric-Binding Site Modulators of beta-Glucocerebrosidase. Authors: Palmer, N. / Agnew, C. / Benn, C. / Buffham, W.J. / Castro, J.N. / Chessari, G. / Clark, M. / Cons, B.D. / Coyle, J.E. / Dawson, L.A. / Hamlett, C.C.F. / Hodson, C. / Holding, F. / Johnson, ...Authors: Palmer, N. / Agnew, C. / Benn, C. / Buffham, W.J. / Castro, J.N. / Chessari, G. / Clark, M. / Cons, B.D. / Coyle, J.E. / Dawson, L.A. / Hamlett, C.C.F. / Hodson, C. / Holding, F. / Johnson, C.N. / Liebeschuetz, J.W. / Mahajan, P. / McCarthy, J.M. / Murray, C.W. / O'Reilly, M. / Peakman, T. / Price, A. / Rapti, M. / Reeks, J. / Schopf, P. / St-Denis, J.D. / Valenzano, C. / Wallis, N.G. / Walser, R. / Weir, H. / Wilsher, N.E. / Woodhead, A. / Bento, C.F. / Tisi, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 43.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9f9zC ![]() 9fa3C ![]() 9fa6C ![]() 9fadC ![]() 9falC ![]() 9fayC ![]() 9fazC ![]() 9fdiC 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61162.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04062, glucosylceramidase, Transferases; Glycosyltransferases; Hexosyltransferases, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl ...References: UniProt: P04062, glucosylceramidase, Transferases; Glycosyltransferases; Hexosyltransferases, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, galactosylceramidase |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / | |
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-Non-polymers , 6 types, 691 molecules ![](data/chem/img/K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Chemical | ChemComp-A1IBO / ~{ | Mass: 366.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20F2N2O2S / Feature type: SUBJECT OF INVESTIGATION #9: 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: 2.13 Å3/Da / Density % sol: 42.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M KSCN 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9126 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→51.44 Å / Num. obs: 127494 / % possible obs: 93.8 % / Redundancy: 3 % / Rrim(I) all: 0.054 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.165→1.268 Å / Num. unique obs: 6375 / Rrim(I) all: 0.607 / % possible all: 65.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.029 Å2
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Refinement step | Cycle: 1 / Resolution: 1.14→51.44 Å
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Refine LS restraints |
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