+Open data
-Basic information
Entry | Database: PDB / ID: 8ekn | ||||||
---|---|---|---|---|---|---|---|
Title | Co-crystal structure of Chaetomium glucosidase with compound 15 | ||||||
Components | Chaetomium alpha glucosidase | ||||||
Keywords | HYDROLASE/INHIBITOR / alpha glucosidase I / Hydrolase / Inhibitor complex / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information mannosyl-oligosaccharide glucosidase / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / protein N-linked glycosylation / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Thermochaetoides thermophila (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Karade, S.S. / Mariuzza, R.A. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2023 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ekn.cif.gz | 326 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ekn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ekn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ekn_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8ekn_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ekn_validation.xml.gz | 58.8 KB | Display | |
Data in CIF | 8ekn_validation.cif.gz | 82.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/8ekn ftp://data.pdbj.org/pub/pdb/validation_reports/ek/8ekn | HTTPS FTP |
-Related structure data
Related structure data | 7r6jC 7rd2C 7revC 8e3jC 8e3pC 8e4iC 8e4kC 8e4zC 8e5uC 8e6gC 8ecwC 8egvC 8ehpC 8eidC 8eleC 8epjC 8epoC 8eprC 8eq7C 8eqxC 8er4C 8etlC 8etoC 8eudC 8eurC 8eutC 8euxC 7t6wS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 93319.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061620 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human) / References: UniProt: G0SFD1 #5: Sugar | ChemComp-NAG / | |
---|
-Non-polymers , 4 types, 424 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.09 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å |
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: 2.29→46.83 Å / Num. obs: 97615 / % possible obs: 99.36 % / Redundancy: 8.9 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.03868 / Net I/σ(I): 9.75 |
Reflection shell | Resolution: 2.29→2.375 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.9202 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 9205 / CC1/2: 0.797 / CC star: 0.942 / Rpim(I) all: 0.3355 / % possible all: 94.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7T6W Resolution: 2.29→46.83 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.671 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 115.56 Å2 / Biso mean: 38.904 Å2 / Biso min: 19.65 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→46.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.293→2.353 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|