1PIG

PIG PANCREATIC ALPHA-AMYLASE COMPLEXED WITH THE OLIGOSACCHARIDE V-1532


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Carbohydrate and protein-based inhibitors of porcine pancreatic alpha-amylase: structure analysis and comparison of their binding characteristics.

Machius, M.Vertesy, L.Huber, R.Wiegand, G.

(1996) J.Mol.Biol. 260: 409-421

  • DOI: 10.1006/jmbi.1996.0410
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of porcine pancreatic alpha-amylase isozyme II (PPA II) in its free form and complexed with the trestatin A derived pseudo-octasaccharide V-1532 have been determined using Patterson search techniques at resolutions of 2.3 and 2 ...

    The crystal structures of porcine pancreatic alpha-amylase isozyme II (PPA II) in its free form and complexed with the trestatin A derived pseudo-octasaccharide V-1532 have been determined using Patterson search techniques at resolutions of 2.3 and 2.2 angstroms, respectively. Seven rings of the competitive inhibitor V-1532 could be detected in the active site region as well as two maltose units in secondary binding sites on the surface. V-1532 occupies the five central sugar binding subsites similar to the PPA/acarbose structure. A sixth ring exists at the reducing end, connecting two symmetry related PPA molecules. The seventh moiety, a 6-hydroxymethylconduritol ring, is located at the non-reducing end. The electron density for this ring is relatively weak, indicating considerable disorder. This study shows that PPA is able to accommodate more than five rings in the active site region, but that additional rings would increase the binding affinity only slightly, which is in accordance with kinetic experiments. A comparison of the structures of free PPA, PPA/V-1532 and PPA/Tendamistat shows the characteristic conformational changes that accompany inhibitor binding and distinguish pseudo-oligosaccharide inhibitors from proteinaceous inhibitors. Although both classes of inhibitors block the sugar binding subsites in the active site region, the extreme specificity and binding affinity of the proteinaceous inhibitors is probably due to an intricate interaction pattern involving areas further away from the catalytic center.


    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
    • The Crystal Structure of Porcine Pancreatic Alpha-Amylase in Complex with the Microbial Inhibitor Tendamistat
      Wiegand, G.,Epp, O.,Huber, R.
      (1995) J.Mol.Biol. 247: 99
    • 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
    • Carbohydrate Binding Sites in a Pancreatic Alpha-Amylase-Substrate Complex, Derived from X-Ray Structure Analysis at 2.1 Angstrom Resolution
      Qian, M.,Haser, R.,Payan, F.
      (1995) Protein Sci. 4: 747
    • Refined Molecular Structure of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution
      Larson, S.B.,Greenwood, A.,Cascio, D.,Day, J.,McPherson, A.
      (1994) J.Mol.Biol. 235: 1560


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-AMYLASE
A
496Sus scrofaMutation(s): 0 
Gene Names: AMY2
EC: 3.2.1.1
Find proteins for P00690 (Sus scrofa)
Go to UniProtKB:  P00690
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
AGL
Query on AGL

Download SDF File 
Download CCD File 
A
4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE
C6 H13 N O4
RJKBJEZZABBYBA-DVKNGEFBSA-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
HMC
Query on HMC

Download SDF File 
Download CCD File 
A
5-HYDROXYMETHYL-CHONDURITOL
C7 H12 O5
PJPGMULJEYSZBS-VZFHVOOUSA-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: 2.2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.500α = 90.00
b = 114.800β = 90.00
c = 118.700γ = 90.00
Software Package:
Software NamePurpose
ROTAVATA)data scaling
X-PLORrefinement
CCP4data scaling
X-PLORphasing
ROTAVATA/AGROVATAdata reduction
MOSFLMdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance