4GJY JMJD5 in complex with N-Oxalylglycine date 2012-08-10
authors Rizzo, P.A.Del., Trievel, R.C.
compound source
symmetry
R_factor
R_Free 0.1609
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.25
ligand CO, MSE, OGA enzyme
Primary referenceCrystal Structure and Functional Analysis of JMJD5 Indicate An Alternate Specificity and Function., Del Rizzo PA, Krishnan S, Trievel RC, Mol Cell Biol. 2012 Jul 30. PMID:22851697
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (128 Kb) [Save to disk]
  • Biological Unit Coordinates (4gjy.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 4GJY
  • CSU: Contacts of Structural Units for 4GJY
  • Structure Factors (6711 Kb)
  • Retrieve 4GJY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GJY from S2C, [Save to disk]
  • Re-refined 4gjy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GJY 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 4GJY
  • 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 4GJY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gjy_A] [4gjy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4GJY: [JmjC ] by SMART
  • Other resources with information on 4GJY
  • Community annotation for 4GJY at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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