8QMU | pdb_00008qmu

The complex of Glycogen Phosphorylase with (-)-Epigallocatechin-3-gallate (EGCG).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.208 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.164 (Depositor) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8QMU

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Evidence for the Quercetin Binding Site of Glycogen Phosphorylase as a Target for Liver-Isoform-Selective Inhibitors against Glioblastoma: Investigation of Flavanols Epigallocatechin Gallate and Epigallocatechin.

Alexopoulos, S.McGawley, M.Mathews, R.Papakostopoulou, S.Koulas, S.Leonidas, D.D.Zwain, T.Hayes, J.M.Skamnaki, V.

(2024) J Agric Food Chem 72: 24070-24081

  • DOI: https://doi.org/10.1021/acs.jafc.4c06920
  • Primary Citation Related Structures: 
    8QMU, 8R52, 8R53, 8R6V

  • PubMed Abstract: 

    Glycogen phosphorylase (GP) is the rate-determining enzyme in glycogenolysis, and its druggability has been extensively studied over the years for the development of therapeutics against type 2 diabetes (T2D) and, more recently, cancer. However, the conservation of binding sites between the liver and muscle isoforms makes the inhibitor selectivity challenging. Using a combination of kinetic, crystallographic, modeling, and cellular studies, we have probed the binding of dietary flavonoids epigallocatechin gallate (EGCG) and epigallocatechin (EGC) to GP isoforms. The structures of rmGPb-EGCG and rmGPb-EGC complexes were determined by X-ray crystallography, showing binding at the quercetin binding site (QBS) in agreement with kinetic studies that revealed both compounds as noncompetitive inhibitors of GP, with EGCG also causing a significant reduction in cell viability and migration of U87-MG glioblastoma cells. Interestingly, EGCG exhibits different binding modes to GP isoforms, revealing QBS as a promising site for GP targeting, offering new opportunities for the design of liver-selective GP inhibitors.


  • Organizational Affiliation
    • Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Larisa 41500, Greece.

Macromolecule Content 

  • Total Structure Weight: 98.45 kDa 
  • Atom Count: 7,409 
  • Modeled Residue Count: 815 
  • Deposited Residue Count: 830 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle form830Oryctolagus cuniculusMutation(s): 1 
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KDH
(Subject of Investigation/LOI)

Query on KDH



Download:Ideal Coordinates CCD File
B [auth A](2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate
C22 H18 O11
WMBWREPUVVBILR-WIYYLYMNSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.208 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.164 (Depositor) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.855α = 90
b = 126.855β = 90
c = 115.428γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
Cootmodel building
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references