5MCB

Glycogen phosphorylase in complex with chlorogenic acid.

• PDB DOI: https://doi.org/10.2210/pdb5MCB/pdb

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


• Deposited: 2016-11-09 Released: 2017-09-20 
• Deposition Author(s): Leonidas, D.D., Stravodimos, G.A., Kyriakis, E., Chatzileontiadou, D.S.M., Kantsadi, A.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.177 
• R-Value Work: 0.138 
• R-Value Observed: 0.140 

Literature

Affinity Crystallography Reveals the Bioactive Compounds of Industrial Juicing Byproducts of Punica granatum for Glycogen Phosphorylase.

Stravodimos, G.A., Kantsadi, A.L., Apostolou, A., Kyriakis, E., Kafaski-Kanelli, V.N., Solovou, T., Gatzona, P., Liggri, P.G.V., Theofanous, S., Gorgogietas, V.A., Kissa, A., Psachoula, C., Lemonakis, A., Chatzileontiadou, D.S.M., Psarra, A.G., Skamnaki, V.T., Haroutounian, S.A., Leonidas, D.D.

(2018) Curr Drug Discov Technol 15: 41-53

• PubMed: 28625148 
• DOI: https://doi.org/10.2174/1570163814666170619091736
• Primary Citation of Related Structures:  
  5MCB


• PubMed Abstract: 
  

  Glycogen phosphorylase (GP) is a pharmaceutical target for the discovery of new antihyperglycaemic agents. Punica granatum is a well-known plant for its potent antioxidant and antimicrobial activities but so far has not been examined for antihyperglycaemic activity.

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Organizational Affiliation: 

Department of Biochemistry and Biotechnology, University of Thessaly, 26 Biopolis 41500 Larissa, Greece.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 95.88 kDa 
• Atom Count: 6,890 
• Modelled Residue Count: 809 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CGG	C [auth A]	Chlorogenic acid C16 H18 O9 CWVRJTMFETXNAD-FWCWNIRPSA-N
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CGG	Binding MOAD:  5MCB	Ki: 2.50e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.177 
• R-Value Work: 0.138 
• R-Value Observed: 0.140 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.95	α = 90
b = 128.95	β = 90
c = 116.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Leonidas, D.D., Stravodimos, G.A., Kyriakis, E., Chatzileontiadou, D.S.M., Kantsadi, A.L.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description