+Open data
-Basic information
Entry | Database: PDB / ID: 7r6j | ||||||
---|---|---|---|---|---|---|---|
Title | Co-crystal structure of Chaetomium glucosidase with compound 1 | ||||||
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 | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.905 Å | ||||||
Authors | Karade, S.S. / Mariuzza, R.A. | ||||||
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 | 7r6j.cif.gz | 351.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7r6j.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7r6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r6j_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7r6j_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7r6j_validation.xml.gz | 69 KB | Display | |
Data in CIF | 7r6j_validation.cif.gz | 102.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/7r6j ftp://data.pdbj.org/pub/pdb/validation_reports/r6/7r6j | HTTPS FTP |
-Related structure data
Related structure data | 7rd2C 7revC 8e3jC 8e3pC 8e4iC 8e4kC 8e4zC 8e5uC 8e6gC 8ecwC 8egvC 8ehpC 8eidC 8eknC 8eleC 8epjC 8epoC 8eprC 8eq7C 8eqxC 8er4C 8etlC 8etoC 8eudC 8eurC 8eutC 8euxC 4j5tS 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 on special symmetry positions |
|
-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.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 #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 |
---|
-Non-polymers , 5 types, 1286 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-BTB / | #7: 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: 3.06 Å3/Da / Density % sol: 59.86 % |
---|---|
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: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2021 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.77 Å / Num. obs: 168664 / % possible obs: 99.35 % / Redundancy: 6.5 % / Biso Wilson estimate: 30.61 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1458 / Rpim(I) all: 0.061 / Net I/σ(I): 9.98 |
Reflection shell | Resolution: 1.905→1.973 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.791 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 16213 / CC1/2: 0.407 / CC star: 0.76 / Rpim(I) all: 0.7917 / % possible all: 95.82 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J5T Resolution: 1.905→46.77 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.382 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 134.8 Å2 / Biso mean: 33.638 Å2 / Biso min: 15.61 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.905→46.77 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.905→1.954 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|