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- PDB-5ied: Murine endoplasmic reticulum alpha-glucosidase II with castanospermine -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ied | |||||||||
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Title | Murine endoplasmic reticulum alpha-glucosidase II with castanospermine | |||||||||
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![]() | HYDROLASE / Enzyme Glycosyl hydrolase GH31 Quality control exoglycosidase | |||||||||
Function / homology | ![]() mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome / negative regulation of neuron projection development ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome / negative regulation of neuron projection development / carbohydrate binding / in utero embryonic development / carbohydrate metabolic process / intracellular membrane-bounded organelle / calcium ion binding / protein-containing complex binding / Golgi apparatus / endoplasmic reticulum / RNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Caputo, A.T. / Roversi, P. / Alonzi, D.S. / Kiappes, J.L. / Zitzmann, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of mammalian ER alpha-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals. Authors: Caputo, A.T. / Alonzi, D.S. / Marti, L. / Reca, I.B. / Kiappes, J.L. / Struwe, W.B. / Cross, A. / Basu, S. / Lowe, E.D. / Darlot, B. / Santino, A. / Roversi, P. / Zitzmann, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 403.6 KB | Display | ![]() |
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PDB format | ![]() | 325.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 66.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5f0eSC ![]() 5h9oC ![]() 5hjoC ![]() 5hjrC ![]() 5ieeC ![]() 5iefC ![]() 5iegC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 106157.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 9568.298 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This chain contains all of the residues from the mature O08795 but has been trypsinised so that there all that was crystallised is: 30-117 Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 1 types, 1 molecules
#3: 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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-Non-polymers , 7 types, 913 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/CTS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/CTS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PG4 / ![]() Source method: isolated from a genetically manipulated source Formula: C8H18O5 Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) ![]() ![]() ![]() #5: Chemical | ChemComp-P6G / ![]() Source method: isolated from a genetically manipulated source Formula: C12H26O7 Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) ![]() ![]() ![]() #6: Chemical | ChemComp-EDO / ![]() Source method: isolated from a genetically manipulated source Formula: C2H6O2 Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) ![]() ![]() ![]() #7: Chemical | ChemComp-FMT / ![]() Source method: isolated from a genetically manipulated source Formula: CH2O2 Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) ![]() ![]() ![]() #8: Chemical | ChemComp-CTS / | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 21% v/v ethylene glycol, 11% w/v PEG 8000 (from the Morpheus Precipitant Mix 2), 50 mM Morpheus carboxylic acids mix, 100 mM Morpheus buffer system 1 pH 6.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→173.9 Å / Num. obs: 103854 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.39 Å2 / CC1/2: 0.996 / Rsym value: 0.186 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.81→1.91 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5F0E Resolution: 1.81→86.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.097
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Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→86.95 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.81 Å / Rfactor Rfree error: 0
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