2QN8

Glycogen Phosphorylase b in complex with N-4-nitrobenzoyl-N'-beta-D-glucopyranosyl urea

Structural Biology Knowledgebase: 2QN8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 2QN8

Classification: TRANSFERASE

Total Structure Weight: 98377.78

Macromolecule Entities
Molecule Chains Length Organism Details
Glycogen phosphorylase, muscle form A 842 Oryctolagus cuniculus EC#: 2.4.1.1 IUBMB
Mutation: L380I
Gene Name(s): PYGM Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N-{[(4-nitrophenyl)carbonyl]carbamoyl}-beta- D-glucopyranosylamine
C14 H17 N3 O9
TXVZHPDFTXBTMX-BZNQNGANSA-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)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NBY Ki: 3300 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.181
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.61 α = 90.00
b = 128.61 β = 90.00
c = 116.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-07-18
  • Released Date: 2008-07-22
  • Deposition author(s): Chrysina, E.D., Tiraidis, C., Alexacou, K.-M., Zographos, S.E., Leonidas, D.D., Oikonomakos, N.G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update