4E8M Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+ date
authors Marcia, M., Pyle, A.M.
compound source
symmetry
R_factor
R_Free 0.28020
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.50
ligand EPE, K, MG, SPM enzyme
Primary referenceVisualizing Group II Intron Catalysis through the Stages of Splicing., Marcia M, Pyle AM, Cell. 2012 Oct 26;151(3):497-507. doi: 10.1016/j.cell.2012.09.033. PMID:23101623
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (365 Kb) [Save to disk]
  • Biological Unit Coordinates (4e8m.pdb1.gz) 357 Kb
  • LPC: Ligand-Protein Contacts for 4E8M
  • CSU: Contacts of Structural Units for 4E8M
  • Structure Factors (358 Kb)
  • Retrieve 4E8M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4E8M from S2C, [Save to disk]
  • Re-refined 4e8m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4E8M 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 4E8M
  • 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 4E8M, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4e8m_A] [4e8m]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4E8M
  • Community annotation for 4E8M at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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