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- PDB-8cb1: 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: 8cb1 | ||||||
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Title | Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with N-PNT-DNM 15 | ||||||
![]() | (Lysosomal alpha-glucosidase ...) x 2 | ||||||
![]() | HYDROLASE / Gaa / Pompe disease / pharmacological chaperone | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Sulzenbacher, G. / Roig-Zamboni, V. / Overkleeft, H. / Artola, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Fluorescence polarisation activity-based protein profiling for the identification of deoxynojirimycin-type inhibitors selective for lysosomal retaining alpha- and beta-glucosidases. Authors: van der Gracht, D. / Rowland, R.J. / Roig-Zamboni, V. / Ferraz, M.J. / Louwerse, M. / Geurink, P.P. / Aerts, J.M.F.G. / Sulzenbacher, G. / Davies, G.J. / Overkleeft, H.S. / Artola, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217.2 KB | Display | ![]() |
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PDB format | ![]() | 164.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 41.1 KB | Display | |
Data in CIF | ![]() | 63.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nwvC ![]() 8cb6C ![]() 5nn3S S: Starting model for refinement 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
-Lysosomal alpha-glucosidase ... , 2 types, 2 molecules GA
#1: Protein | Mass: 14095.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FULL-LENGTH RHGAA HAS BEEN TREATED WITH CHYMOTRYPSIN, LEADING TO A SAMPLE STARTING AT RESIDUE GLN81. MISSING SURFACE LOOPS HAVE EQUALLY BEEN REMOVED BY PROTEOLYTIC CLEAVAGE. Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 82901.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FULL-LENGTH RHGAA HAS BEEN TREATED WITH CHYMOTRYPSIN, LEADING TO A SAMPLE STARTING AT RESIDUE GLN81. MISSING SURFACE LOOPS HAVE EQUALLY BEEN REMOVED BY PROTEOLYTIC CLEAVAGE. Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 4 types, 5 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: 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 #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Non-polymers , 7 types, 812 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/U4X.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/U4X.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-GOL / #9: Chemical | #10: Chemical | ChemComp-EDO / #11: Chemical | ChemComp-U4X / ( | #12: Chemical | ChemComp-SO4 / #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 62.79 % |
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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 |
-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: Sep 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.38 Å / Num. obs: 129900 / % possible obs: 100 % / Redundancy: 15.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.031 / Rrim(I) all: 0.124 / Χ2: 0.97 / Net I/σ(I): 14.1 / Num. measured all: 2029400 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 15 % / Rmerge(I) obs: 2.065 / Num. unique obs: 6355 / CC1/2: 0.573 / Rpim(I) all: 0.537 / Rrim(I) all: 2.135 / Χ2: 0.91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NN3 Resolution: 1.75→47.73 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.83 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.587 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→47.73 Å
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Refine LS restraints |
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