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- PDB-5nn5: 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: 5nn5 | |||||||||
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Title | Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with 1-deoxynojirimycin | |||||||||
![]() | Lysosomal alpha-glucosidase | |||||||||
![]() | HYDROLASE / glycoside hydrolase / lysosome / glycogen catabolism / Pompe disease | |||||||||
Function / homology | ![]() vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-1,4-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / alpha-glucosidase activity / alpha-glucosidase / glycophagy / diaphragm contraction ...vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-1,4-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / alpha-glucosidase activity / alpha-glucosidase / glycophagy / diaphragm contraction / neuromuscular process controlling posture / maltose alpha-glucosidase activity / tissue development / regulation of the force of heart contraction / glycogen catabolic process / aorta development / azurophil granule membrane / Glycogen breakdown (glycogenolysis) / muscle cell cellular homeostasis / lysosome organization / tertiary granule membrane / neuromuscular process controlling balance / 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 | ![]() ![]() ![]() | |||||||||
![]() | Roig-Zamboni, V. / Cobucci-Ponzano, B. / Iacono, R. / Ferrara, M.C. / Germany, S. / Parenti, G. / Bourne, Y. / Moracci, M. | |||||||||
![]() | ![]() Title: Structure of human lysosomal acid alpha-glucosidase-a guide for the treatment of Pompe disease. Authors: Roig-Zamboni, V. / Cobucci-Ponzano, B. / Iacono, R. / Ferrara, M.C. / Germany, S. / Bourne, Y. / Parenti, G. / Moracci, M. / Sulzenbacher, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359.3 KB | Display | ![]() |
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PDB format | ![]() | 287.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 38.1 KB | Display | |
Data in CIF | ![]() | 59.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nn3SC ![]() 5nn4C ![]() 5nn6C ![]() 5nn8C 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 , 1 types, 1 molecules A
#1: Protein | Mass: 96978.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | 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 #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-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 , 5 types, 791 molecules ![](data/chem/img/NOJ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-NOJ / | ||||||
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#7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-EDO / #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.73 % |
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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 pH 7.0, 2% v/v PEG400 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2014 |
Radiation | Monochromator: 0.8726 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2→53.86 Å / Num. obs: 83609 / % possible obs: 95.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 14.22 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.125 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2 / Num. unique obs: 4552 / CC1/2: 0.675 / Rpim(I) all: 0.426 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NN3 Resolution: 2→53.86 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.245 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.493 Å2
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Refinement step | Cycle: 1 / Resolution: 2→53.86 Å
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Refine LS restraints |
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