› 2g9v

X-ray diffraction
2.15Å resolution

The crystal structure of glycogen phosphorylase in complex with (3R,4R,5R)-5-hydroxymethylpiperidine-3,4-diol and phosphate

Released:
DOI: 10.2210/pdb2g9v/pdb
PDB entry 2g9v coloured by chain, front view.
PDB entry 2g9v coloured by chain, side view.
PDB entry 2g9v coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
Iminosugars as potential inhibitors of glycogenolysis: structural insights into the molecular basis of glycogen phosphorylase inhibition.
Oikonomakos NG, Tiraidis C, Leonidas DD, Zographos SE, Kristiansen M, Jessen CU, Nørskov-Lauritsen L, Agius L
J Med Chem 49 5687-701 (2006)
PMID: 16970395

Function and Biology Details

Reaction catalysed: 
((1->4)-alpha-D-glucosyl)(n) + phosphate = ((1->4)-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132556 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycogen phosphorylase, muscle form Chain: A
Molecule details ›
Chain: A
Length: 842 amino acids
Theoretical weight: 97.52 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: P00489 (Residues: 2-843; Coverage: 100%)
Gene name: PYGM
Sequence domains: Carbohydrate phosphorylase
Structure domains: Glycogen Phosphorylase B;

Ligands and Environments

2 bound ligands:
Ligand PO4 2 x PO4
Ligand IFM 1 x IFM
1 modified residue:
Ligand LLP 1 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P43212
Unit cell:
a: 128.636Å b: 128.636Å c: 116.455Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.193 0.235

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Citations

3 review citations

New hepatic targets for glycaemic control in diabetes.
Agius L. (2007)
2 more