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 
  • R-Value Observed: 0.140 

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
  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle formA825Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CGG
Query on CGG

Download Ideal Coordinates CCD File 
C [auth A]Chlorogenic acid
C16 H18 O9
CWVRJTMFETXNAD-FWCWNIRPSA-N
 Ligand Interaction
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CGGKi:  2500000   nM  Binding MOAD
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 = 128.95α = 90
b = 128.95β = 90
c = 116.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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