5MEM | pdb_00005mem

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

  • Classification: FLUORESCENT PROTEIN
  • Organism(s): Oryctolagus cuniculus
  • Mutation(s): No 

  • 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 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5MEM

Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1002/chem.201701591
  • Primary Citation Related Structures: 
    5MEM

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 98.14 kDa 
  • Atom Count: 6,930 
  • Modeled Residue Count: 807 
  • Deposited Residue Count: 843 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle form843Oryctolagus cuniculusMutation(s): 0 
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
7LS

Query on 7LS


Download:Ideal Coordinates CCD File
C [auth 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
PLP

Query on PLP


Download:Ideal Coordinates CCD File
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.195 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.363α = 90
b = 128.363β = 90
c = 116.512γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references, Structure summary