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Yorodumi- PDB-5emy: Human Pancreatic Alpha-Amylase in complex with the mechanism base... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5emy | ||||||||||||
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Title | Human Pancreatic Alpha-Amylase in complex with the mechanism based inactivator glucosyl epi-cyclophellitol | ||||||||||||
Components | Pancreatic alpha-amylase | ||||||||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / Amylase / Diabetes / Obesity / Glucosyl hydrolase / HYDROLASE-HYDROLASE inhibitor complex | ||||||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.231 Å | ||||||||||||
Authors | Caner, S. / Brayer, G.D. | ||||||||||||
Funding support | Canada, 1items
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Citation | Journal: Febs Lett. / Year: 2016 Title: Glucosyl epi-cyclophellitol allows mechanism-based inactivation and structural analysis of human pancreatic alpha-amylase. Authors: Caner, S. / Zhang, X. / Jiang, J. / Chen, H.M. / Nguyen, N.T. / Overkleeft, H. / Brayer, G.D. / 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 | 5emy.cif.gz | 313.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5emy.ent.gz | 256.5 KB | Display | PDB format |
PDBx/mmJSON format | 5emy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/5emy ftp://data.pdbj.org/pub/pdb/validation_reports/em/5emy | HTTPS FTP |
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-Related structure data
Related structure data | 4x9yS 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 / Fragment: UNP residues 16-511 Source method: isolated from a genetically manipulated source Details: The residue (XEP) is a modified Aspartate with the complexed Glucosyl-epi-cyclophellitol Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Organ: Pancreas / Production host: Komagataella pastoris (fungus) / References: UniProt: P04746, alpha-amylase |
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#2: Sugar | ChemComp-5QP / ( |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | The authors state that the starting material of the ligand is Glucosyl-epi-cyclophellitol |
-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: 40.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM sodium cacodylate, 58% MPD, obtained crystals were soaked in 100mM glucosyl epi-cyclophellitol solution and incubated for up to two weeks to allow complex formation. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→36.65 Å / Num. all: 134773 / Num. obs: 134741 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.54 |
Reflection shell | Resolution: 1.23→1.26 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.02 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X9Y Resolution: 1.231→36.648 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.231→36.648 Å
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Refine LS restraints |
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LS refinement shell |
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