2AMV

THE STRUCTURE OF GLYCOGEN PHOSPHORYLASE B WITH AN ALKYL-DIHYDROPYRIDINE-DICARBOXYLIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of glycogen phosphorylase b with an alkyldihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor.

Zographos, S.E.Oikonomakos, N.G.Tsitsanou, K.E.Leonidas, D.D.Chrysina, E.D.Skamnaki, V.T.Bischoff, H.Goldmann, S.Watson, K.A.Johnson, L.N.

(1997) Structure 5: 1413-1425

  • DOI: 10.1016/s0969-2126(97)00292-x
  • Primary Citation of Related Structures:  
    2AMV

  • PubMed Abstract: 
  • In muscle and liver, glycogen concentrations are regulated by the reciprocal activities of glycogen phosphorylase (GP) and glycogen synthase. An alkyl-dihydropyridine-dicarboxylic acid has been found to be a potent inhibitor of GP, and as such has potential to contribute to the regulation of glycogen metabolism in the non-insulin-dependent diabetes diseased state ...

    In muscle and liver, glycogen concentrations are regulated by the reciprocal activities of glycogen phosphorylase (GP) and glycogen synthase. An alkyl-dihydropyridine-dicarboxylic acid has been found to be a potent inhibitor of GP, and as such has potential to contribute to the regulation of glycogen metabolism in the non-insulin-dependent diabetes diseased state. The inhibitor has no structural similarity to the natural regulators of GP. We have carried out structural studies in order to elucidate the mechanism of inhibition.


    Related Citations: 
    • Effects of Commonly Used Cryoprotectants on Glycogen Phosphorylase Activity and Structure
      Tsitsanou, K.E., Oikonomakos, N.G., Zographos, S.E., Skamnaki, V.T., Gregoriou, M., Watson, K.A., Johnson, L.N., Fleet, G.W.
      (1999) Protein Sci 8: 741
    • Glycogen Phosphorylase B: Description of the Protein Structure
      Acharya, K.R., Stuart, D.I., Varvill, K.M., Johnson, L.N.
      (1991) Glycogen Phosphorylase B: Description Of The Protein Structure --: 1
    • Crystallographic Binding Studies on the Allosteric Inhibitor Glucose-6- Phosphate to T State Glycogen Phosphorylase b
      Johnson, L.N., Snape, P., Martin, J.L., Acharya, K.R., Barford, D., Oikonomakos, N.G.
      (1993) J Mol Biol 232: 253

    Organizational Affiliation

    Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation 48, vas Constantinou Avenue, Athens, 11635, Greece.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (GLYCOGEN PHOSPHORYLASE)A842Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BIN
Query on BIN

Download Ideal Coordinates CCD File 
C [auth A]2,3-DICARBOXY-4-(2-CHLORO-PHENYL)-1-ETHYL-5-ISOPROPOXYCARBONYL-6-METHYL-PYRIDINIUM
C20 H21 Cl N O6
HMSIYRVIPQHZBI-UHFFFAOYSA-O
 Ligand Interaction
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BINKi:  1.600000023841858   nM  Binding MOAD
BINKi :  1.600000023841858   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.11α = 90
b = 127.11β = 90
c = 115.46γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance