2PRJ

Binding of N-acetyl-beta-D-glucopyranosylamine to Glycogen Phosphorylase B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 2PRJ

Classification: TRANSFERASE

Total Structure Weight: 98107.76

Macromolecule Entities
Molecule Chains Length Organism Details
GLYCOGEN PHOSPHORYLASE A 842 Oryctolagus cuniculus EC#: 2.4.1.1 IUBMB
Mutation: L380I, P609A
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
IMP
Query on IMP

A INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-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)
NBG
Query on NBG

A 1-N-ACETYL-BETA-D-GLUCOSAMINE
C8 H15 N O6
IBONACLSSOLHFU-JAJWTYFOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NBG Ki: 31623 - 32000 nM (97 - 99) BindingDB

Ki: 32000 nM  BindingMOAD
Ki: 32000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.181
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.50 α = 90.00
b = 128.50 β = 90.00
c = 116.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-12-11
  • Released Date: 1998-12-16
  • Deposition author(s): Oikonomakos, N.G., Kontou, M., Zographos, S.E., Watson, K.A., Johnson, L.N., Bichard, C.J.F., Fleet, G.W.J., Acharya, K.R.
  • Previous versions: 1PRJ

Revision History

  • 2008-04-26
    Type: Version format compliance
  • 2011-07-13
    Type: Derived calculations, Version format compliance