2AMV

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

• PDB DOI:  https://doi.org/10.2210/pdb2AMV/pdb
• Entry: 2AMV supersedes: 1AMV

• Classification: TRANSFERASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 1998-10-13 Released: 1998-10-21 
• Deposition Author(s): Zographos, S.E., Oikonomakos, N.G., Johnson, L.N.

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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 

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

• PubMed: 9384557 
• DOI: https://doi.org/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. 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 98.04 kDa 
• Atom Count: 7,350 
• Modelled Residue Count: 829 
• Deposited Residue Count: 842 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GLYCOGEN PHOSPHORYLASE)	A	842	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: PYGM EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489  Go to UniProtKB:  P00489

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BIN	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
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BIN	PDBBind:  2AMV	Ki: 1.6 (nM) from 1 assay(s)
	Binding MOAD:  2AMV	Ki: 1.6 (nM) from 1 assay(s)

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 = 127.11	α = 90
b = 127.11	β = 90
c = 115.46	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-21 
Deposition Author(s): Zographos, S.E., Oikonomakos, N.G., Johnson, L.N.
• This entry supersedes: 1AMV

Revision History  

• 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