2AMV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.282 
  • R-Value Work: 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

  • Also Cited By: 1Z62, 1WV1, 1WV0, 1WUY, 1WUT, 1E1Y

  • 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 po ...

    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: 
    • 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
    • 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


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GLYCOGEN PHOSPHORYLASE)
A
842Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
Find proteins for P00489 (Oryctolagus cuniculus)
Go to Gene View: PYGM
Go to UniProtKB:  P00489
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BIN
Query on BIN

Download SDF File 
Download CCD File 
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 SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BINKi: 1.6 nM BINDINGMOAD
BINKi: 1.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 127.110α = 90.00
b = 127.110β = 90.00
c = 115.460γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORphasing
X-PLORmodel building
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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