5MEM

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

• PDB DOI: https://doi.org/10.2210/pdb5MEM/pdb

• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

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

• PubMed: 28493496 
• DOI: https://doi.org/10.1002/chem.201701591
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	843	Oryctolagus cuniculus	Mutation(s): 0  EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489  Go to UniProtKB:  P00489

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7LS	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	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7LS	Binding MOAD:  5MEM	Ki: 71 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.363	α = 90
b = 128.363	β = 90
c = 116.512	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Mamais, M., Chrysina, E.D.

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Funding Organization	Location	Grant Number
European Social Fund, Greek National Strategic Reference Framework (NSRF) - Research Funding Program: Heracleitus II	Greece	Heracleitus II -MIS:346942
European Union	Greece	245866
European Union	Germany	283570

Revision History  

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