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Yorodumi- PDB-3l4u: Crystal complex of N-terminal Human Maltase-Glucoamylase with de-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l4u | |||||||||
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Title | Crystal complex of N-terminal Human Maltase-Glucoamylase with de-O-sulfonated kotalanol | |||||||||
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 / alpha-glucosidase / maltose catabolic process / 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 / alpha-glucosidase / maltose catabolic process / 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: 1.9 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 | 3l4u.cif.gz | 196.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l4u.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 3l4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l4u_validation.pdf.gz | 1002.1 KB | Display | wwPDB validaton report |
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Full document | 3l4u_full_validation.pdf.gz | 1015.8 KB | Display | |
Data in XML | 3l4u_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 3l4u_validation.cif.gz | 57.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/3l4u ftp://data.pdbj.org/pub/pdb/validation_reports/l4/3l4u | HTTPS FTP |
-Related structure data
Related structure data | 3l4tC 3l4vC 3l4wC 3l4xC 3l4yC 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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Details | biological unit is the same as asym. |
-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 , 3 types, 598 molecules
#3: Chemical | ChemComp-DSK / ( |
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#5: Chemical | ChemComp-SO4 / |
#6: 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: 2.7 Å3/Da / Density % sol: 54.45 % |
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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 19, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9175 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. obs: 84175 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.121 / Χ2: 1.146 / Net I/σ(I): 8.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.917 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.134 / 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: 64.43 Å2 / Biso mean: 21.744 Å2 / Biso min: 8.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.905→1.954 Å / Total num. of bins used: 20
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