5MEM

A potent fluorescent inhibitor of glycogen phosphorylase as a catalytic site probe.

  • Classification: FLUORESCENT PROTEIN
  • Organism(s): Oryctolagus cuniculus

  • Deposited: 2016-11-15 Released: 2017-11-29 
  • Deposition Author(s): Mamais, M., Chrysina, E.D.
  • Funding Organization(s): European Social Fund, Greek National Strategic Reference Framework (NSRF) - Research Funding Program: Heracleitus II; European Union 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A New Potent Inhibitor of Glycogen Phosphorylase Reveals the Basicity of the Catalytic Site.

Mamais, M.Degli Esposti, A.Kouloumoundra, V.Gustavsson, T.Monti, F.Venturini, A.Chrysina, E.D.Markovitsi, D.Gimisis, T.

(2017) Chemistry 23: 8800-8805

  • DOI: 10.1002/chem.201701591

  • PubMed Abstract: 
  • The design and synthesis of a glucose-based acridone derivative (GLAC), a potent inhibitor of glycogen phosphorylase (GP) are described. GLAC is the first inhibitor of glycogen phosphorylase, the electronic absorption properties of which are clearly ...

    The design and synthesis of a glucose-based acridone derivative (GLAC), a potent inhibitor of glycogen phosphorylase (GP) are described. GLAC is the first inhibitor of glycogen phosphorylase, the electronic absorption properties of which are clearly distinguishable from those of the enzyme. This allows probing subtle interactions in the catalytic site. The GLAC absorption spectra, associated with X-ray crystallography and quantum chemistry calculations, reveal that part of the catalytic site of GP behaves as a highly basic environment in which GLAC exists as a bis-anion. This is explained by water-bridged hydrogen-bonding interactions with specific catalytic site residues.


    Organizational Affiliation

    Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
843Oryctolagus cuniculusMutation(s): 0 
Gene 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7LS
Query on 7LS

Download SDF File 
Download CCD File 
A
2-[[1-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-10~{H}-acridin-9-one
C23 H22 N4 O7
GFASNZAXNSUSSV-RECXWPGBSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.363α = 90.00
b = 128.363β = 90.00
c = 116.512γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Social Fund, Greek National Strategic Reference Framework (NSRF) - Research Funding Program: Heracleitus IIGreeceHeracleitus II -MIS:346942
European UnionGreece245866
European UnionGermany283570

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release