7ONF

The binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship between structural data and effects on cell metabolome

• PDB DOI: https://doi.org/10.2210/pdb7ONF/pdb

• Classification: TRANSFERASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2021-05-25 Released: 2022-04-06 
• Deposition Author(s): Tsagkarakou, A.S., Koulas, S.M., Kyriakis, E., Drakou, C.E., Leonidas, D.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.161 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 

Starting Model: experimental

Literature

Structure activity relationship of the binding of p-coumaroyl glucose to glycogen phosphorylase and its effect on hepatic cell metabolic pathways

Tsagkarakou, A.S., Chasapi, S.A., Koulas, S.M., Tsialtas, I., Kyriakis, E., Drakou, C.E., Kun, S., Somsak, L., Spyroulias, G.A., Psarra, A.M.G., Leonidas, D.D.

(2021) Eur J Med Chem Rep 3: 100011

• DOI: https://doi.org/10.1016/j.ejmcr.2021.100011

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)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 96.2 kDa 
• Atom Count: 7,160 
• Modelled Residue Count: 810 
• Deposited Residue Count: 825 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	825	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMP	C [auth A]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
VKK (Subject of Investigation/LOI)	D [auth A]	p-coumaroyl glucose C15 H18 O8 DSNCQKUYZOSARM-QVLXMGEUSA-N
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.161 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.607	α = 90
b = 128.607	β = 90
c = 116.633	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Tsagkarakou, A.S., Koulas, S.M., Kyriakis, E., Drakou, C.E., Leonidas, D.D.

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description