1PIG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 3.0 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:  
    1PIG, 1PIF

  • 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 2.2 angstroms, respectively ...

    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 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
    • 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
    • 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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-AMYLASE A496Sus scrofaMutation(s): 0 
Gene Names: AMY2
EC: 3.2.1.1
Find proteins for P00690 (Sus scrofa)
Explore P00690 
Go to UniProtKB:  P00690
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
C
3 N/A Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
D
2 N/A Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download Ideal Coordinates CCD File 
A
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
HMC
Query on HMC

Download Ideal Coordinates CCD File 
A
5-HYDROXYMETHYL-CHONDURITOL
C7 H12 O5
PJPGMULJEYSZBS-VZFHVOOUSA-N
 Ligand Interaction
CA
Query on CA

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

Download Ideal Coordinates CCD File 
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
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Dalpha-maltoseOligosaccharide /  Nutrient

--

Entity ID: 5
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900023
Query on PRD_900023
Ealpha-cellobioseOligosaccharide /  Metabolism

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.5α = 90
b = 114.8β = 90
c = 118.7γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2019-12-25
    Changes: Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary