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- PDB-9gtc: Crystal structure of human lysosomal acid-alpha-glucosidase, GAA,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9gtc | ||||||
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Title | Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 4g | ||||||
![]() | Lysosomal alpha-glucosidase | ||||||
![]() | HYDROLASE / acid-alpha-glucosidase / lysosomal / iminosugar / Pompe disease | ||||||
Function / homology | ![]() vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / alpha-1,4-glucosidase activity / alpha-glucosidase / neuromuscular process controlling posture / glycophagy ...vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / alpha-1,4-glucosidase activity / alpha-glucosidase / neuromuscular process controlling posture / glycophagy / tissue development / diaphragm contraction / regulation of the force of heart contraction / glycogen catabolic process / aorta development / azurophil granule membrane / lysosome organization / neuromuscular process controlling balance / Glycogen breakdown (glycogenolysis) / muscle cell cellular homeostasis / tertiary granule membrane / ficolin-1-rich granule membrane / heart morphogenesis / cardiac muscle contraction / lysosomal lumen / locomotory behavior / glucose metabolic process / carbohydrate binding / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sulzenbacher, G. / Roig-Zamboni, V. / Moracci, M. / Parenti, G. / Py, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: C -Branched Iminosugars as Selective Pharmacological Chaperones of Lysosomal alpha-Glucosidase for the Treatment of Pompe Disease. Authors: Vieira Da Cruz, A. / Perraudin, V. / Minopoli, N. / Iacono, R. / Roig-Zamboni, V. / Bossio, A. / Tangara, S. / Fayolle, M. / Kanazawa, A. / Philouze, C. / Tarallo, A. / Heming, J.J.A. / ...Authors: Vieira Da Cruz, A. / Perraudin, V. / Minopoli, N. / Iacono, R. / Roig-Zamboni, V. / Bossio, A. / Tangara, S. / Fayolle, M. / Kanazawa, A. / Philouze, C. / Tarallo, A. / Heming, J.J.A. / Artola, M. / Behr, J.B. / Overkleeft, H.S. / Moracci, M. / Sulzenbacher, G. / Parenti, G. / Py, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 37.3 KB | Display | |
Data in CIF | ![]() | 52.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9gsvC ![]() 9gswC ![]() 9gtdC ![]() 9gtlC ![]() 9gtnC ![]() 9gttC ![]() 9gtwC 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 105448.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 5 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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, 247 molecules 










#5: Chemical | ChemComp-A1IO7 / ( Mass: 233.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23NO4 / Feature type: SUBJECT OF INVESTIGATION | ||||||||||
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#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-GOL / #9: Chemical | #10: Chemical | ChemComp-EDO / #11: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9 M AMMONIUM SULPHATE, 0.1 M HEPES, 2% V/V PEG400, PH 7 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980114 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→48.64 Å / Num. obs: 41193 / % possible obs: 99.1 % / Redundancy: 9.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.069 / Rrim(I) all: 0.213 / Χ2: 0.99 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.58→2.69 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.091 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4245 / CC1/2: 0.706 / Rpim(I) all: 0.374 / Rrim(I) all: 1.155 / Χ2: 1.04 |
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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: 31.596 Å2
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Refinement step | Cycle: 1 / Resolution: 2.58→48.64 Å
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Refine LS restraints |
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