1JFH

STRUCTURE OF A PANCREATIC ALPHA-AMYLASE BOUND TO A SUBSTRATE ANALOGUE AT 2.03 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.

Qian, M.Spinelli, S.Driguez, H.Payan, F.

(1997) Protein Sci. 6: 2285-2296

  • DOI: 10.1002/pro.5560061102
  • Also Cited By: 1VAH

  • PubMed Abstract: 
  • The structure of pig pancreatic alpha-amylase in complex with carbohydrate inhibitor and proteinaceous inhibitors is known but the successive events occurring at the catalytic center still remain to be elucidated. The X-ray structure analysis of a cr ...

    The structure of pig pancreatic alpha-amylase in complex with carbohydrate inhibitor and proteinaceous inhibitors is known but the successive events occurring at the catalytic center still remain to be elucidated. The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC 3.2.1.1.) soaked with an enzyme-resistant substrate analogue, methyl 4,4'-dithio-alpha-maltotrioside, showed electron density corresponding to the binding of substrate analogue molecules at the active site and at the "second binding site." The electron density observed at the active site was interpreted in terms of overlapping networks of oligosaccharides, which show binding of substrate analogue molecules at subsites prior to and subsequent to the cleavage site. A weaker patch of density observed at subsite -1 (using a nomenclature where the site of hydrolysis is taken to be between subsites -1 and +1) was modeled with water molecules. Conformational changes take place upon substrate analogue binding and the "flexible loop" that constitutes the surface edge of the active site is observed in a specific conformation. This confirms that this loop plays an important role in the recognition and binding of the ligand. The crystal structure was refined at 2.03 A resolution, to an R-factor of 16.0 (Rfree, 18.5).


    Related Citations: 
    • The Active Center of a Mammalian Alpha-Amylase. Structure of the Complex of a Pancreatic Alpha-Amylase with a Carbohydrate Inhibitor Refined to 2.2-A Resolution
      Qian, M.,Haser, R.,Buisson, G.,Duee, E.,Payan, F.
      (1994) Biochemistry 33: 6284
    • Carbohydrate Binding Sites in a Pancreatic Alpha-Amylase-Substrate Complex, Derived from X-Ray Structure Analysis at 2.1 A Resolution
      Qian, M.,Haser, R.,Payan, F.
      (1995) Protein Sci. 4: 747
    • Crystal Structure of Pig Pancreatic Alpha-Amylase Isoenzyme II, in Complex with the Carbohydrate Inhibitor Acarbose
      Gilles, C.,Astier, J.P.,Marchis-Mouren, G.,Cambillau, C.,Payan, F.
      (1996) Eur.J.Biochem. 238: 561
    • Structure and Molecular Model Refinement of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution
      Qian, M.,Haser, R.,Payan, F.
      (1993) J.Mol.Biol. 231: 785


    Organizational Affiliation

    AFMB-IBSM-CNRS, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-AMYLASE
A
496Sus scrofaGene Names: AMY2
EC: 3.2.1.1
Find proteins for P00690 (Sus scrofa)
Go to UniProtKB:  P00690
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MA1
Query on MA1

Download SDF File 
Download CCD File 
A
1,4-dithio-alpha-D-glucopyranose
C6 H12 O4 S2
MUOMBPNNVXJUGT-QZABAPFNSA-N
 Ligand Interaction
MA2
Query on MA2

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Download CCD File 
A
4-S-methyl-4-thio-alpha-D-glucopyranose
C7 H14 O5 S
UYUQSQYXZFSOEM-GKHCUFPYSA-N
 Ligand Interaction
CL
Query on CL

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

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

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Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
MA3
Query on MA3

Download SDF File 
Download CCD File 
A
O1-METHYL-4-DEOXY-4-THIO-ALPHA-D-GLUCOSE
C7 H14 O5 S
PFROTWRHYMLGHR-GKHCUFPYSA-N
 Ligand Interaction
HG
Query on HG

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Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.300α = 90.00
b = 87.800β = 90.00
c = 103.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-09-19 
  • Released Date: 1998-12-02 
  • Deposition Author(s): Qian, M., Payan, F.

Revision History 

  • Version 1.0: 1998-12-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance