4YOY Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dT and Mg2+ ion date
authors Miyazono, K., Ito, T., Tanokura, M.
compound source
symmetry
R_factor
R_Free 0.2042
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.95
ligand MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, E
  • exonuclease activity


    • Primary referenceStructural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I., Miyazono KI, Ishino S, Tsutsumi K, Ito T, Ishino Y, Tanokura M, Nucleic Acids Res. 2015 Jul 2. pii: gkv654. PMID:26138487
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (243 Kb) [Save to disk]
  • Biological Unit Coordinates (4yoy.pdb1.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 4YOY
  • CSU: Contacts of Structural Units for 4YOY
  • Structure Factors (1069 Kb)
  • Retrieve 4YOY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YOY from S2C, [Save to disk]
  • Re-refined 4yoy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4YOY 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 4YOY
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yoy_E] [4yoy] [4yoy_B] [4yoy_D] [4yoy_F] [4yoy_C] [4yoy_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4YOY
  • Community annotation for 4YOY at PDBWiki (http://pdbwiki.org)

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