1XL1

Kinetic and crystallographic studies on 2-(beta-D-glucopyranosyl)-5-methyl-1,3,4-oxadiazole,-benzothiazole, and-benzimidazole, inhibitors of muscle glycogen phosphorylase b. Evidence for a new binding site.

Structural Biology Knowledgebase: 1XL1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 1XL1

Classification: TRANSFERASE

Total Structure Weight: 97850.48

Macromolecule Entities
Molecule Chains Length Organism Details
Glycogen phosphorylase, muscle form A 842 Oryctolagus cuniculus EC#: 2.4.1.1 IUBMB
Gene Name(s): PYGM Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TH1
Query on TH1

A 2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-BENZOTHIAZOLE
3, (Synonym)
C14 H17 N O5 S
WGJFWQVWYRZPEP-KABOQKQYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLP
Query on PLP

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TH1 Ki: 76000 nM (100) BindingDB

Ki: 76000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.181
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.11 α = 90.00
b = 128.11 β = 90.00
c = 115.45 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-09-30
  • Released Date: 2005-03-15
  • Deposition author(s): Chrysina, E.D., Kosmopoulou, M.N., Tiraidis, C., Kardakaris, R., Bischler, N., Leonidas, D.D., Hadady, Z., Somsak, L., Docsa, T., Gergely, P., Oikonomakos, N.G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values