1B2Y

STRUCTURE OF HUMAN PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH THE CARBOHYDRATE INHIBITOR ACARBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structures of human pancreatic alpha-amylase in complex with carbohydrate and proteinaceous inhibitors.

Nahoum, V.Roux, G.Anton, V.Rouge, P.Puigserver, A.Bischoff, H.Henrissat, B.Payan, F.

(2000) Biochem.J. 346 Pt 1: 201-208


  • PubMed Abstract: 
  • Crystal structures of human pancreatic alpha-amylase (HPA) in complex with naturally occurring inhibitors have been solved. The tetrasaccharide acarbose and a pseudo-pentasaccharide of the trestatin family produced identical continuous electron densi ...

    Crystal structures of human pancreatic alpha-amylase (HPA) in complex with naturally occurring inhibitors have been solved. The tetrasaccharide acarbose and a pseudo-pentasaccharide of the trestatin family produced identical continuous electron densities corresponding to a pentasaccharide species, spanning the -3 to +2 subsites of the enzyme, presumably resulting from transglycosylation. Binding of the acarviosine core linked to a glucose residue at subsites -1 to +2 appears to be a critical part of the interaction process between alpha-amylases and trestatin-derived inhibitors. Two crystal forms, obtained at different values of pH, for the complex of HPA with the protein inhibitor from Phaseolus vulgaris (alpha-amylase inhibitor) have been solved. The flexible loop typical of the mammalian alpha-amylases was shown to exist in two different conformations, suggesting that loop closure is pH-sensitive. Structural information is provided for the important inhibitor residue, Arg-74, which has not been observed previously in structural analyses.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, CNRS-IFR1, 31 Chemin Joseph Aiguier, 13402 Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ALPHA-AMYLASE)
A
496Homo sapiensGene Names: AMY2A
EC: 3.2.1.1
Find proteins for P04746 (Homo sapiens)
Go to Gene View: AMY2A
Go to UniProtKB:  P04746
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AC1
Query on AC1

Download SDF File 
Download CCD File 
A
6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL
N-[4-HYDROXYMETHYL-CYCLOHEXAN-6-YL-1,2,3-TRIOL]-4,6-DIDEOXY-4-AMINOGLUCOPYRANOSIDE
C13 H23 N O8
RBZIIHWPZWOIDU-ZCGMLSCUSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
PCA
Query on PCA

Download SDF File 
Download CCD File 
A
PYROGLUTAMIC ACID
C5 H7 N O3
ODHCTXKNWHHXJC-VKHMYHEASA-N
 Ligand Interaction
G6D
Query on G6D

Download SDF File 
Download CCD File 
A
6-DEOXY-ALPHA-D-GLUCOSE
D-Quinovose
C6 H12 O5
SHZGCJCMOBCMKK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.110α = 90.00
b = 75.100β = 90.00
c = 137.130γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-12-03 
  • Released Date: 2000-02-16 
  • Deposition Author(s): Nahoum, V., Payan, F.

Revision History 

  • Version 1.0: 2000-02-16
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2017-10-25
    Type: Atomic model, Structure summary