5EMY | pdb_00005emy

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

• PDB DOI: https://doi.org/10.2210/pdb5EMY/pdb

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2015-11-06 Released: 2016-07-06 
• Deposition Author(s): Caner, S., Brayer, G.D.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

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

• PubMed: 27000970 
• DOI: https://doi.org/10.1002/1873-3468.12143
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pancreatic alpha-amylase	A	496	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5QP	B [auth A]	(1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside C13 H24 O10 POWCVSWKDOOEBI-FELRGSJNSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free:  0.142 (Depositor), 0.140 (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 = 52.33	α = 90
b = 68.18	β = 90
c = 130.38	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Caner, S., Brayer, G.D.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	CIHR MOP-111082

Revision History  

• 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