4EDZ Crystal structure of hH-PGDS with water displacing inhibitor date 2012-03-27
authors Day, J.E., Thorarensen, A., Trujillo, J.I.
compound source
symmetry
R_factor
R_Free 0.2360
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.00
ligand 0O5, GSH, MG BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceInvestigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): A tale of two waters., Trujillo JI, Kiefer JR, Huang W, Day JE, Moon J, Jerome GM, Bono CP, Kornmeier CM, Williams ML, Kuhn C, Rennie GR, Wynn TA, Carron CP, Thorarensen A, Bioorg Med Chem Lett. 2012 Jun 1;22(11):3795-9. Epub 2012 Apr 13. PMID:22546671
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (284 Kb) [Save to disk]
  • Biological Unit Coordinates (4edz.pdb1.gz) 139 Kb
  • Biological Unit Coordinates (4edz.pdb2.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 4EDZ
  • CSU: Contacts of Structural Units for 4EDZ
  • Structure Factors (1141 Kb)
  • Retrieve 4EDZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4EDZ from S2C, [Save to disk]
  • Re-refined 4edz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4EDZ 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 4EDZ
  • 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 4EDZ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4edz_B] [4edz_C] [4edz_A] [4edz] [4edz_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4EDZ
  • Community annotation for 4EDZ at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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