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Yorodumi- PDB-3cpu: SUBSITE MAPPING OF THE ACTIVE SITE OF HUMAN PANCREATIC ALPHA-AMYL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cpu | ||||||||||||
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Title | SUBSITE MAPPING OF THE ACTIVE SITE OF HUMAN PANCREATIC ALPHA-AMYLASE USING SUBSTRATES, THE PHARMACOLOGICAL INHIBITOR ACARBOSE, AND AN ACTIVE SITE VARIANT | ||||||||||||
Components | Pancreatic alpha-amylase | ||||||||||||
Keywords | HYDROLASE / AMYLASE / ACARBOSE / MUTAGENESIS / DIABETES / CATALYSIS / PANCREATIC / ENZYME / HUMAN | ||||||||||||
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: 2 Å | ||||||||||||
Authors | Brayer, G.D. / Sidhu, G. / Maurus, R. / Rydberg, E.H. / Braun, C. / Wang, Y. / Nguyen, N.T. / Overall, C.M. / Withers, S.G. | ||||||||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Subsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques. Authors: Brayer, G.D. / Sidhu, G. / Maurus, R. / Rydberg, E.H. / Braun, C. / Wang, Y. / Nguyen, N.T. / Overall, C.M. / Withers, S.G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cpu.cif.gz | 115.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cpu.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 3cpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/3cpu ftp://data.pdbj.org/pub/pdb/validation_reports/cp/3cpu | HTTPS FTP |
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-Related 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: 55930.320 Da / Num. of mol.: 1 / Mutation: D300N Source method: isolated from a genetically manipulated source Details: A PART OF ACARBOSE INHIBITOR, DISACCHARIDE GLC(499)-GLC(500) CHAIN B, OBSERVED AT ACTIVE SITE Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Organ: PANCREAS / Production host: Pichia pastoris (fungus) / References: UniProt: P04746, alpha-amylase |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-CL / |
#5: 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: 2.43 Å3/Da / Density % sol: 49.3 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 31361 / % possible obs: 83.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 119912 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.2 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→8 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å |