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Yorodumi- PDB-2qmj: Crystral Structure of the N-terminal Subunit of Human Maltase-Glu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qmj | |||||||||
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Title | Crystral Structure of the N-terminal Subunit of Human Maltase-Glucoamylase in Complex with Acarbose | |||||||||
Components | Maltase-glucoamylase, intestinal | |||||||||
Keywords | HYDROLASE / Glycosyl Hydrolase Family 31 / Glycoprotein / Glycosidase / Membrane / Multifunctional enzyme / 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: 1.9 Å | |||||||||
Authors | Sim, L. / Rose, D.R. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Human intestinal maltase-glucoamylase: crystal structure of the N-terminal catalytic subunit and basis of inhibition and substrate specificity Authors: Sim, L. / Quezada-Calvillo, R. / Sterchi, E.E. / Nichols, B.L. / 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 | 2qmj.cif.gz | 204.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qmj.ent.gz | 159 KB | Display | PDB format |
PDBx/mmJSON format | 2qmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qmj ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qmj | HTTPS FTP |
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-Related structure data
Related structure data | 2qlySC S: Starting model for refinement 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 | The biological assembly is a monomer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 98585.992 Da / Num. of mol.: 1 / Fragment: SEQUENCE DATABASE RESIDUES 87-954 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGAM, MGA, MGAML / Plasmid: pMT-BiP-V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells References: UniProt: O43451, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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-Sugars , 3 types, 4 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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#3: Polysaccharide | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose |
#4: Sugar |
-Non-polymers , 3 types, 636 molecules
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.33 % |
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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, 4% 1,1,1,3,3,3-hexafluoro-2-propanol, 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: May 19, 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: 1.9→30 Å / Num. obs: 82234 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rsym value: 0.109 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 7898 / Rsym value: 0.401 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QLY Resolution: 1.9→19.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.081 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.132 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.108 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.943 Å / Total num. of bins used: 20
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