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Open data
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Basic information
Entry | Database: PDB / ID: 8epr | ||||||
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Title | Co-crystal structure of Chaetomium glucosidase with compound 19 | ||||||
![]() | Chaetomium alpha glucosidase | ||||||
![]() | HYDROLASE/INHIBITOR / alpha glucosidase I / Hydrolase / Inhibitor complex / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() mannosyl-oligosaccharide glucosidase / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / protein N-linked glycosylation / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karade, S.S. / Mariuzza, R.A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum alpha-Glucosidase I with Anti-SARS-CoV-2 Activity. Authors: Karade, S.S. / Franco, E.J. / Rojas, A.C. / Hanrahan, K.C. / Kolesnikov, A. / Yu, W. / MacKerell Jr., A.D. / Hill, D.C. / Weber, D.J. / Brown, A.N. / Treston, A.M. / Mariuzza, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 348.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 69.7 KB | Display | |
Data in CIF | ![]() | 102.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r6jC ![]() 7rd2C ![]() 7revC ![]() 8e3jC ![]() 8e3pC ![]() 8e4iC ![]() 8e4kC ![]() 8e4zC ![]() 8e5uC ![]() 8e6gC ![]() 8ecwC ![]() 8egvC ![]() 8ehpC ![]() 8eidC ![]() 8eknC ![]() 8eleC ![]() 8epjC ![]() 8epoC ![]() 8eq7C ![]() 8eqxC ![]() 8er4C ![]() 8etlC ![]() 8etoC ![]() 8eudC ![]() 8eurC ![]() 8eutC ![]() 8euxC ![]() 7t6wS S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 93319.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 5 types, 1288 molecules ![](data/chem/img/WSW.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-BTB / | #7: 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: 2.92 Å3/Da / Density % sol: 57.88 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 Bis Tris pH 6.5, 1.6-2.0 M Ammonium sulfate |
-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: Jun 11, 2021 |
Radiation | Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→46.78 Å / Num. obs: 148613 / % possible obs: 98.83 % / Redundancy: 9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0817 / Rpim(I) all: 0.02848 / Net I/σ(I): 11.69 |
Reflection shell | Resolution: 1.99→2.061 Å / Rmerge(I) obs: 0.7393 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 14375 / CC1/2: 0.855 / Rpim(I) all: 0.2531 / % possible all: 97.31 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7T6W Resolution: 1.99→46.78 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.648 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 111.2 Å2 / Biso mean: 31.627 Å2 / Biso min: 15.05 Å2
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Refinement step | Cycle: final / Resolution: 1.99→46.78 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 25513 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.99→2.039 Å / Rfactor Rfree error: 0
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