1B4D

AMIDOCARBAMATE INHIBITOR OF GLYCOGEN PHOSPHORYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure.

Tsitsanou, K.E.Oikonomakos, N.G.Zographos, S.E.Skamnaki, V.T.Gregoriou, M.Watson, K.A.Johnson, L.N.Fleet, G.W.

(1999) Protein Sci. 8: 741-749

  • DOI: 10.1110/ps.8.4.741
  • Primary Citation of Related Structures:  1BX3

  • PubMed Abstract: 
  • The effects of a number of cryoprotectants on the kinetic and structural properties of glycogen phosphorylase b have been investigated. Kinetic studies showed that glycerol, one of the most commonly used cryoprotectants in X-ray crystallographic stud ...

    The effects of a number of cryoprotectants on the kinetic and structural properties of glycogen phosphorylase b have been investigated. Kinetic studies showed that glycerol, one of the most commonly used cryoprotectants in X-ray crystallographic studies, is a competitive inhibitor with respect to substrate glucose-1-P with an apparent Ki value of 3.8% (v/v). Cryogenic experiments, with the enzyme, have shown that glycerol binds at the catalytic site and competes with glucose analogues that bind at the catalytic site, thus preventing the formation of complexes. This necessitated a change in the conditions for cryoprotection in crystallographic binding experiments with glycogen phosphorylase. It was found that 2-methyl-2,4-pentanediol (MPD), polyethylene glycols (PEGs) of various molecular weights, and dimethyl sulfoxide (DMSO) activated glycogen phosphorylase b to different extents, by stabilizing its most active conformation, while sucrose acted as a noncompetitive inhibitor and ethylene glycol as an uncompetitive inhibitor with respect to glucose-1-P. A parallel experimental investigation by X-ray crystallography showed that, at 100 K, both MPD and DMSO do not bind at the catalytic site, do not induce any significant conformational change on the enzyme molecule, and hence, are more suitable cryoprotectants than glycerol for binding studies with glycogen phosphorylase.


    Related Citations: 
    • Stereospecific Synthesis of Spirohydantoins of Beta-Glucopyranose:Inhibitors of Glycogen Phosphorylase
      Krulle, T.M.,De La Fuente, C.,Watson, K.A.,Gregoriou, M.,Johnson, L.N.,Tsitsanou, K.E.,Zographos, S.E.,Oikonomakos, N.G.,Fleet, G.W.J.
      (1997) Synlett --: 211
    • Glucose Analogue Inhibitors of Glycogen Phosphorylase: The Design of Potential Drugs for Diabetes
      Martin, J.L.,Veluraja, K.,Ross, K.,Johnson, L.N.,Fleet, G.W.,Ramsden, N.G.,Bruce, I.,Orchard, M.G.,Oikonomakos, N.G.,Papageorgiou, A.C.,Leonidas, D.D.,Tsitoura, H.S.
      (1991) Biochemistry 30: 10101
    • N-Acetyl-Beta-D-Glucopyranosylamine:A Potent T-State Inhibitor of Glycogen Phosphorylase. A Comparison with Alpha-D-Glucose
      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.
      (1995) Protein Sci. 4: 2469


    Organizational Affiliation

    Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, Athens, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GLYCOGEN PHOSPHORYLASE B)
A
842Oryctolagus cuniculusGene Names: PYGM
EC: 2.4.1.1
Find proteins for P00489 (Oryctolagus cuniculus)
Go to Gene View: PYGM
Go to UniProtKB:  P00489
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download SDF File 
Download CCD File 
A
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
CRA
Query on CRA

Download SDF File 
Download CCD File 
A
1-DEOXY-1-METHOXYCARBAMIDO-BETA-D-GLUCO-2-HEPTULOPYRANOSONAMIDE
C9 H16 N2 O8
ZQTAMPRAONLFQI-FMTWGGRWSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CRAKi: 15849 - 16000 nM (97) BINDINGDB
CRAKi: 15600 nM BINDINGMOAD
CRAKi: 15600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 126.680α = 90.00
b = 126.680β = 90.00
c = 115.350γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
CCP4model building
CCP4phasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance