3BD7

Glycogen Phosphorylase complex with 1(-D-glucopyranosyl) thymine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b

Cisma, C.Sovantzis, D.A.Hadjiloi, T.Stathis, D.Gimisis, T.Hayes, J.M.Zographos, S.E.Leonidas, D.D.Chrysina, E.D.Oikonomakos, N.G.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
842Oryctolagus 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
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
CKB
Query on CKB

Download SDF File 
Download CCD File 
A
1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione
1-D-glucopyranosyl-thymine
C11 H16 N2 O7
RMXUFBPORJBBEZ-HPFNVAMJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CKBIC50: 6600 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 127.963α = 90.00
b = 127.963β = 90.00
c = 116.230γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
ADSCdata collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance