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Yorodumi- PDB-1b2y: STRUCTURE OF HUMAN PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH THE C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b2y | |||||||||||||||
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Title | STRUCTURE OF HUMAN PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH THE CARBOHYDRATE INHIBITOR ACARBOSE | |||||||||||||||
Components | Pancreatic alpha-amylase | |||||||||||||||
Keywords | HYDROLASE / HUMAN ALPHA-AMYLASE / ACARBOSE | |||||||||||||||
Function / homology | Function and homology information polysaccharide digestion / Digestion of dietary carbohydrate / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular exosome / extracellular region Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||||||||
Authors | Nahoum, V. / Payan, F. | |||||||||||||||
Citation | Journal: Biochem.J. / Year: 2000 Title: Crystal structures of human pancreatic alpha-amylase in complex with carbohydrate and proteinaceous inhibitors. Authors: Nahoum, V. / Roux, G. / Anton, V. / Rouge, P. / Puigserver, A. / Bischoff, H. / Henrissat, B. / Payan, F. | |||||||||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR-DETERMINED | |||||||||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR-DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b2y.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b2y.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 1b2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b2y_validation.pdf.gz | 433.7 KB | Display | wwPDB validaton report |
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Full document | 1b2y_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 1b2y_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 1b2y_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/1b2y ftp://data.pdbj.org/pub/pdb/validation_reports/b2/1b2y | HTTPS FTP |
-Related structure data
Related structure data | 1hnyS 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
#1: Protein | Mass: 55931.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PANCREAS / References: UniProt: P04746, alpha-amylase |
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#2: Polysaccharide | alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6- ...alpha-D-quinovopyranose-(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)-beta-D-glucopyranose Type: oligosaccharide / Mass: 791.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | PYRROLIDON |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||
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Crystal grow | pH: 8 / Details: 60% 2-METHYLPENTAN-2,4 DIOL, pH 8.0 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Date: Jul 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→25 Å / Num. obs: 10103 / % possible obs: 91.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 3.2→3.27 Å / Redundancy: 9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5.7 / % possible all: 63.4 |
Reflection | *PLUS Num. measured all: 45084 |
Reflection shell | *PLUS % possible obs: 63.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HNY Resolution: 3.2→11 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 1.0E-5 / σ(F): 1
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Displacement parameters | Biso mean: 9.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.34 Å / Total num. of bins used: 8
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