5MCB

Glycogen phosphorylase in complex with chlorogenic acid.


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.2174/1570163814666170619091736

  • 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 antihypergly ...

    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.


    Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, 26 Biopolis 41500 Larissa, Greece.,Department of Animal Sciences and Aquaculture, Agricultural University of Athens, Athens, Iera Odos 75, 11855 Athens, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
825Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
Find proteins for P00489 (Oryctolagus cuniculus)
Go to Gene View: PYGM
Go to UniProtKB:  P00489
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CGG
Query on CGG

Download SDF File 
Download CCD File 
A
Chlorogenic acid
C16 H18 O9
CWVRJTMFETXNAD-FWCWNIRPSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CGGKi: 2500000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.138 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.950α = 90.00
b = 128.950β = 90.00
c = 116.720γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references