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Yorodumi- PDB-3ole: Structures of human pancreatic alpha-amylase in complex with acar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ole | ||||||||||||
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Title | Structures of human pancreatic alpha-amylase in complex with acarviostatin II03 | ||||||||||||
Components | Pancreatic alpha-amylase | ||||||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / glycosylation / HYDROLASE-HYDROLASE INHIBITOR complex / Acarviostatin II03 | ||||||||||||
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 / SYNCHROTRON / SAD / Resolution: 1.55 Å | ||||||||||||
Authors | Qin, X. / Ren, L. | ||||||||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Structures of human pancreatic alpha-amylase in complex with acarviostatins: Implications for drug design against type II diabetes. Authors: Qin, X. / Ren, L. / Yang, X. / Bai, F. / Wang, L. / Geng, P. / Bai, G. / Shen, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ole.cif.gz | 132.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ole.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ole.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ole_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3ole_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3ole_validation.xml.gz | 26 KB | Display | |
Data in CIF | 3ole_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/3ole ftp://data.pdbj.org/pub/pdb/validation_reports/ol/3ole | HTTPS FTP |
-Related structure data
Related structure data | 3oldC 3olgC 3oliC 1b2yS C: citing same article (ref.) 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: 55980.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04746, alpha-amylase |
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-Sugars , 5 types, 5 molecules
#2: Polysaccharide | alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
#5: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltotriose |
#9: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 537 molecules
#6: Chemical | ChemComp-CA / | ||||||
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#7: Chemical | ChemComp-CL / | ||||||
#8: Chemical | ChemComp-SO4 / | ||||||
#10: Chemical | #11: Chemical | ChemComp-PCA / | #12: Chemical | ChemComp-MPD / ( | #13: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | ACARVIOSTA |
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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: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 60% 2-methylpentan-2,4 diol, 100mM cacodylate pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 30, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→26.16 Å / Num. all: 67514 / Num. obs: 67254 / % possible obs: 98.1 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 / Biso Wilson estimate: 14.2 Å2 |
Reflection shell | Resolution: 1.55→1.59 Å / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: 1B2Y Resolution: 1.55→26.16 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1836671.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.1401 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→26.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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