5OX3

Glycogen Phosphorylase in complex with SzB102v


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Probing the beta-pocket of the active site of human liver glycogen phosphorylase with 3-(C-beta-d-glucopyranosyl)-5-(4-substituted-phenyl)-1, 2, 4-triazole inhibitors.

Kyriakis, E.Solovou, T.G.A.Kun, S.Czifrak, K.Szocs, B.Juhasz, L.Bokor, E.Stravodimos, G.A.Kantsadi, A.L.Chatzileontiadou, D.S.M.Skamnaki, V.T.Somsak, L.Leonidas, D.D.

(2018) Bioorg. Chem. 77: 485-493


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
843Oryctolagus 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download SDF File 
Download CCD File 
A
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
B1N
Query on B1N

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Download CCD File 
A
(2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[3-(4-hydroxyphenyl)-1~{H}-1,2,4-triazol-5-yl]oxane-3,4,5-triol
C14 H17 N3 O6
YFAQQSHHRSTJJB-RMPHRYRLSA-N
 Ligand Interaction
PLP
Query on PLP

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Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.134 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.550α = 90.00
b = 128.550β = 90.00
c = 116.190γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release