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Yorodumi- PDB-1hx0: Structure of pig pancreatic alpha-amylase complexed with the "tru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hx0 | |||||||||||||||
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Title | Structure of pig pancreatic alpha-amylase complexed with the "truncate" acarbose molecule (pseudotrisaccharide) | |||||||||||||||
Components | ALPHA AMYLASE (PPA) | |||||||||||||||
Keywords | HYDROLASE / Alpha-amylase / inhibitor / carbohydrate / pancreas | |||||||||||||||
Function / homology | Function and homology information alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | |||||||||||||||
Biological species | Sus scrofa (pig) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | |||||||||||||||
Authors | Qian, M. / Payan, F. | |||||||||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Enzyme-catalyzed condensation reaction in a mammalian alpha-amylase. High-resolution structural analysis of an enzyme-inhibitor complex Authors: Qian, M. / Nahoum, V. / Bonicel, J. / Bischoff, H. / Henrissat, B. / Payan, F. #1: Journal: Eur.J.Biochem. / Year: 1996 Title: Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose Authors: Gilles, C. / Astier, J.P. / Marchis-Mouren, G. / Cambillau, C. / Payan, F. #2: Journal: Biochemistry / Year: 1994 Title: The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution Authors: Qian, M. / Haser, R. / Buisson, G. / Duee, E. / Payan, F. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hx0.cif.gz | 269.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hx0.ent.gz | 217.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/1hx0 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/1hx0 | HTTPS FTP |
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-Related structure data
Related structure data | 1ppiS S: Starting model for refinement |
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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: 55472.828 Da / Num. of mol.: 1 / Mutation: Q16PCA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Tissue: PANCREAS / Production host: Escherichia coli (E. coli) / References: UniProt: P00690, alpha-amylase |
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-Sugars , 2 types, 2 molecules
#2: 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)-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 Type: oligosaccharide / Mass: 948.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-Non-polymers , 4 types, 938 molecules
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | RESIDUE GLC 1993 AND GBC 2993 ARE IN ALTERNATE CONFORMATI |
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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: 4.15 Å3/Da / Density % sol: 70.38 % |
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Crystal grow | Temperature: 277 K / Method: batch / pH: 8.5 / Details: CaCl2, pH 8.5, batch, temperature 277K |
Crystal grow | *PLUS Details: Qian, M., (1993) J. Mol. Biol., 232, 785. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 1999 |
Radiation | Monochromator: bouble-diamond crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→35 Å / Num. all: 189616 / Num. obs: 184003 / % possible obs: 97.04 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.38→1.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.93 / Num. unique all: 16627 / % possible all: 96.13 |
Reflection | *PLUS Num. measured all: 507677 |
Reflection shell | *PLUS % possible obs: 96.13 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PPI Resolution: 1.38→35 Å / Cross valid method: throughout FREE R / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.38→35 Å
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 1 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.38 Å / Lowest resolution: 1.42 Å / Num. reflection obs: 47628 |