› 4mi9

X-ray diffraction
1.85Å resolution

Crystal structure of Gpb in complex with SUGAR (N-[(3R)-3-(4-ETHYLPHENYL)BUTANOYL]-BETA-D-GLUCOPYRANOSYLAMINE) (S20)

Released:
DOI: 10.2210/pdb4mi9/pdb
PDB entry 4mi9 coloured by chain, front view.
PDB entry 4mi9 coloured by chain, side view.
PDB entry 4mi9 coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
Structure based inhibitor design targeting glycogen phosphorylase B. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-β-d-glucopyranosylamines.
Parmenopoulou V, Kantsadi AL, Tsirkone VG, Chatzileontiadou DS, Manta S, Zographos SE, Molfeta C, Archontis G, Agius L, Hayes JM, Leonidas DD, Komiotis D
Bioorg Med Chem 22 4810-25 (2014)
PMID: 25092521

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 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: 825 amino acids
Theoretical weight: 95.51 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: P00489 (Residues: 13-837; Coverage: 98%)
Gene name: PYGM
Sequence domains: Carbohydrate phosphorylase
Structure domains: Glycogen Phosphorylase B;

Ligands and Environments

1 bound ligand:
Ligand 26W 1 x 26W
1 modified residue:
Ligand LLP 1 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-2
Spacegroup: P43212
Unit cell:
a: 128.81Å b: 128.81Å c: 116.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.162 0.19

Quick links

Citations

3 review citations

Regulation of pyruvate metabolism and human disease.
Gray et al. (2014)
2 more

1 mention without citation

Proteomics Reveals an Increase in the Abundance of Glycolytic and Ethanolic Fermentation Enzymes in Developing Sugarcane Culms During Sucrose Accumulation.
Boaretto et al. (2021)