› 1k08

X-ray diffraction
2.26Å resolution

Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to glycogen phosphorylase b

Released:
DOI: 10.2210/pdb1k08/pdb
PDB entry 1k08 coloured by chain, front view.
PDB entry 1k08 coloured by chain, side view.
PDB entry 1k08 coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies.
Oikonomakos NG, Kosmopoulou M, Zographos SE, Leonidas DD, Chrysina ED, Somsák L, Nagy V, Praly JP, Docsa T, Tóth B, Gergely P
Eur J Biochem 269 1684-96 (2002)
PMID: 11895439

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: 97.29 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


Cofactor: Ligand PLP 1 x PLP
1 bound ligand:
Ligand BZD 2 x BZD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P43212
Unit cell:
a: 128.519Å b: 128.519Å c: 116.497Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.18 0.212

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Citations

1 review citation

In the Search of Glycoside-Based Molecules as Antidiabetic Agents.
Pałasz et al. (2019)
31 other articles