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Yorodumi- PDB-3l4y: Crystal complex of N-terminal Human Maltase-Glucoamylase with NR4-8II -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l4y | |||||||||
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Title | Crystal complex of N-terminal Human Maltase-Glucoamylase with NR4-8II | |||||||||
Components | Maltase-glucoamylase, intestinal | |||||||||
Keywords | HYDROLASE / Glycoside Hydrolase Family 31 / Cell membrane / Disulfide bond / Glycoprotein / Glycosidase / Membrane / Multifunctional enzyme / Polymorphism / Signal-anchor / Sulfation / Transmembrane | |||||||||
Function / homology | Function and homology information amylase activity / dextrin catabolic process / alpha-1,4-glucosidase activity / glucan 1,4-alpha-glucosidase activity / maltose catabolic process / alpha-glucosidase / maltose alpha-glucosidase activity / starch catabolic process / Digestion of dietary carbohydrate / tertiary granule membrane ...amylase activity / dextrin catabolic process / alpha-1,4-glucosidase activity / glucan 1,4-alpha-glucosidase activity / maltose catabolic process / alpha-glucosidase / maltose alpha-glucosidase activity / starch catabolic process / Digestion of dietary carbohydrate / tertiary granule membrane / ficolin-1-rich granule membrane / catalytic activity / carbohydrate binding / apical plasma membrane / Neutrophil degranulation / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Sim, L. / Rose, D.R. | |||||||||
Citation | Journal: Biochemistry / Year: 2010 Title: New glucosidase inhibitors from an ayurvedic herbal treatment for type 2 diabetes: structures and inhibition of human intestinal maltase-glucoamylase with compounds from Salacia reticulata. Authors: Sim, L. / Jayakanthan, K. / Mohan, S. / Nasi, R. / Johnston, B.D. / Pinto, B.M. / Rose, D.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l4y.cif.gz | 203.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l4y.ent.gz | 162 KB | Display | PDB format |
PDBx/mmJSON format | 3l4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/3l4y ftp://data.pdbj.org/pub/pdb/validation_reports/l4/3l4y | HTTPS FTP |
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-Related structure data
Related structure data | 3l4tC 3l4uC 3l4vC 3l4wC 3l4xC 3l4zC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 99276.742 Da / Num. of mol.: 1 / Fragment: UNP residues 87-954 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGA, MGAM, MGAML / Plasmid: pMT-BiP-V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells References: UniProt: O43451, alpha-glucosidase, glucan 1,4-alpha-glucosidase |
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-Sugars , 2 types, 3 molecules
#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 |
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#4: Sugar |
-Non-polymers , 4 types, 808 molecules
#3: Chemical | ChemComp-NR4 / ( | ||||
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#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.2M sodium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9175 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9175 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30 Å / Num. obs: 95952 / % possible obs: 98.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.109 / Χ2: 1.488 / Net I/σ(I): 15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.91 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.92 Å2 / Biso mean: 23.982 Å2 / Biso min: 8.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Total num. of bins used: 20
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