4OD5 Substrate-bound structure of a UbiA homolog from Aeropyrum pernix K1 date 2014-01-10
authors Li, W., Cheng, W.
compound source
symmetry
R_factor
R_Free 0.3014
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.56
ligand GST, MG, PHB enzyme
Gene APE
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructural insights into ubiquinone biosynthesis in membranes., Cheng W, Li W, Science. 2014 Feb 21;343(6173):878-81. doi: 10.1126/science.1246774. PMID:24558159
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (516 Kb) [Save to disk]
  • Biological Unit Coordinates (4od5.pdb1.gz) 86 Kb
  • Biological Unit Coordinates (4od5.pdb2.gz) 86 Kb
  • Biological Unit Coordinates (4od5.pdb3.gz) 87 Kb
  • Biological Unit Coordinates (4od5.pdb4.gz) 87 Kb
  • Biological Unit Coordinates (4od5.pdb5.gz) 88 Kb
  • Biological Unit Coordinates (4od5.pdb6.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 4OD5
  • CSU: Contacts of Structural Units for 4OD5
  • Structure Factors (1258 Kb)
  • Retrieve 4OD5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4OD5 from S2C, [Save to disk]
  • Re-refined 4od5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4OD5 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 4OD5
  • 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 4OD5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4od5_A] [4od5_C] [4od5_D] [4od5_F] [4od5_E] [4od5] [4od5_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4OD5
  • Community annotation for 4OD5 at PDBWiki (http://pdbwiki.org)

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