1OSE

Porcine pancreatic alpha-amylase complexed with acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

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: 561-569

  • DOI: 10.1111/j.1432-1033.1996.0561z.x
  • Primary Citation of Related Structures:  
    1OSE

  • PubMed Abstract: 
  • Two different crystal forms of pig pancreatic alpha-amylase isoenzyme II (PPAII), free and complexed to a carbohydrate inhibitor (acarbose), have been compared together and to previously reported structures of PPAI. A crystal form obtained at 4 degrees C, containing nearly 72% solvent, made it possible to obtain a new complex with acarbose, different from a previous one obtained at 20 degrees C [Qian, M ...

    Two different crystal forms of pig pancreatic alpha-amylase isoenzyme II (PPAII), free and complexed to a carbohydrate inhibitor (acarbose), have been compared together and to previously reported structures of PPAI. A crystal form obtained at 4 degrees C, containing nearly 72% solvent, made it possible to obtain a new complex with acarbose, different from a previous one obtained at 20 degrees C [Qian, M., Buisson, G., Duée, E., Haser, H. & Payan, F. (1994) Biochemistry 33, 6284-6294]. In the present form, six contiguous subsites of the enzyme active site are occupied by the carbohydrate ligand; the structural data indicate that the binding site is capable of holding more than the five glucose units of the scheme proposed through kinetic studies. A monosaccharide ring bridging two protein molecules related by the crystal packing is located on the surface, at a distance of 2.0 nm from the reducing end of the inhibitor ligand; the symmetry-related glucose ring in the crystal lattice is found 1.5 nm away from the non-reducing end of the inhibitor ligand.


    Related Citations: 
    • 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
    • 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
    • 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

    LCCMB-IBSM, CNRS, Marseille, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PORCINE ALPHA-AMYLASEA496Sus scrofaMutation(s): 0 
Gene Names: AMY2
EC: 3.2.1.1
UniProt
Find proteins for P00690 (Sus scrofa)
Explore P00690 
Go to UniProtKB:  P00690
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranoseB4N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G94545JA
GlyCosmos:  G94545JA
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC (Subject of Investigation/LOI)
Query on BGC

Download Ideal Coordinates CCD File 
C [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.6α = 90
b = 114.7β = 90
c = 118.5γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 1996-03-20 
  • Released Date: 1997-04-01 
  • Deposition Author(s): Gilles, C., Payan, F.

Revision History  (Full details and data files)

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Data collection, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary