3L7D Transferase date Dec 28, 2009
title Crystal Structure Of Glycogen Phosphorylase Dk5 Complex
authors V.G.Tsirkone, C.Lamprakis, J.M.Hayes, V.Skamnaki, C.Drakou, S.E.Z D.D.Leonidas
compound source
Molecule: Glycogen Phosphorylase, Muscle Form
Chain: A
Synonym: Myophosphorylase
Ec: 2.4.1.1
 Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986
symmetry Space Group: P 43 21 2
R_factor 0.184 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
129.132 129.132 117.010 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand DK5, LLP enzyme Transferase E.C.2.4.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary reference1-(3-Deoxy-3-fluoro-beta-d-glucopyranosyl) pyrimidine derivatives as inhibitors of glycogen phosphorylase b: Kinetic, crystallographic and modelling studies., Tsirkone VG, Tsoukala E, Lamprakis C, Manta S, Hayes JM, Skamnaki VT, Drakou C, Zographos SE, Komiotis D, Leonidas DD, Bioorg Med Chem. 2010 May 15;18(10):3413-25. Epub 2010 Apr 7. PMID:20430629
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (3l7d.pdb1.gz) 271 Kb
  • LPC: Ligand-Protein Contacts for 3L7D
  • CSU: Contacts of Structural Units for 3L7D
  • Structure Factors (1000 Kb)
  • Retrieve 3L7D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L7D from S2C, [Save to disk]
  • Re-refined 3l7d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3L7D in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3L7D
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3L7D, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l7d] [3l7d_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3L7D
  • Community annotation for 3L7D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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