5AKN THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE non-CODING STRAND B AND IN THE PRESENCE OF 2MM MN date
authors Molina, R., Marcaida, M.J., Redondo, P., Marenchino, M., Abramo, M.D., Montoya, G., Prieto, J.
compound source
symmetry
R_factor
R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.75
ligand MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, K
  • nuclease activity
  • endonuclease activity


    • Primary referenceEngineering a nickase on the homing endonuclease I-DmoI scaffold., Molina R, Marcaida MJ, Redondo P, Marenchino M, Duchateau P, D'Abramo M, Montoya G, Prieto J, J Biol Chem. 2015 Jun 4. pii: jbc.M115.658666. PMID:26045557
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (329 Kb) [Save to disk]
  • Biological Unit Coordinates (5akn.pdb1.gz) 107 Kb
  • Biological Unit Coordinates (5akn.pdb2.gz) 109 Kb
  • Biological Unit Coordinates (5akn.pdb3.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 5AKN
  • CSU: Contacts of Structural Units for 5AKN
  • Structure Factors (541 Kb)
  • Retrieve 5AKN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5AKN from S2C, [Save to disk]
  • Re-refined 5akn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5AKN 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 5AKN
  • 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 5AKN, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5akn_F] [5akn_M] [5akn_A] [5akn_D] [5akn_B] [5akn_E] [5akn_O] [5akn_H] [5akn_G] [5akn] [5akn_C] [5akn_K] [5akn_J] [5akn_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5AKN
  • Community annotation for 5AKN at PDBWiki (http://pdbwiki.org)

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