5EMY | pdb_00005emy

Human Pancreatic Alpha-Amylase in complex with the mechanism based inactivator glucosyl epi-cyclophellitol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 
    0.142 (Depositor), 0.144 (DCC) 
  • R-Value Work: 
    0.119 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 
    0.120 (Depositor) 

Starting Model: experimental
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This is version 3.2 of the entry. See complete history. 

Literature

Glucosyl epi-cyclophellitol allows mechanism-based inactivation and structural analysis of human pancreatic alpha-amylase.

Caner, S., Zhang, X., Jiang, J., Chen, H.M., Nguyen, N.T., Overkleeft, H., Brayer, G.D., Withers, S.G.

(2016) FEBS Lett 590: 1143-1151

  • DOI: https://doi.org/10.1002/1873-3468.12143
  • Primary Citation Related Structures: 
    5EMY

  • PubMed Abstract: 

    As part of a search for selective, mechanism-based covalent inhibitors of human pancreatic α-amylase we describe the chemoenzymatic synthesis of the disaccharide analog α-glucosyl epi-cyclophellitol, demonstrate its stoichiometric reaction with human pancreatic α-amylase and evaluate the time dependence of its inhibition. X-ray crystallographic analysis of the covalent derivative so formed confirms its reaction at the active site with formation of a covalent bond to the catalytic nucleophile D197. The structure illuminates the interactions with the active site and confirms OH4' on the nonreducing end sugar as a good site for attachment of fluorescent tags in generating probes for localization and quantitation of amylase in vivo.

    • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.

Macromolecule Content 

  • Total Structure Weight: 56.35 kDa 
  • Atom Count: 4,561 
  • Modeled Residue Count: 496 
  • Deposited Residue Count: 496 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pancreatic alpha-amylase496Homo sapiensMutation(s): 0 
Gene Names: AMY2A
EC: 3.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04746 (Homo sapiens)
Explore P04746 
Go to UniProtKB:  P04746
PHAROS:  P04746
GTEx:  ENSG00000243480 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04746
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free:  0.142 (Depositor), 0.144 (DCC) 
  • R-Value Work:  0.119 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 0.120 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.33α = 90
b = 68.18β = 90
c = 130.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaCIHR MOP-111082

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 2.0: 2020-01-08
    Changes: Author supporting evidence, Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 3.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 3.2: 2024-10-23
    Changes: Structure summary