5AK9 THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA 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 0.2224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.60
ligand ACT, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, J, E
  • 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] (328 Kb) [Save to disk]
  • Biological Unit Coordinates (5ak9.pdb1.gz) 107 Kb
  • Biological Unit Coordinates (5ak9.pdb2.gz) 108 Kb
  • Biological Unit Coordinates (5ak9.pdb3.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 5AK9
  • CSU: Contacts of Structural Units for 5AK9
  • Structure Factors (638 Kb)
  • Retrieve 5AK9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5AK9 from S2C, [Save to disk]
  • Re-refined 5ak9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5AK9 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 5AK9
  • 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 5AK9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ak9_C] [5ak9_D] [5ak9_N] [5ak9_J] [5ak9] [5ak9_K] [5ak9_G] [5ak9_H] [5ak9_F] [5ak9_L] [5ak9_A] [5ak9_B] [5ak9_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5AK9
  • Community annotation for 5AK9 at PDBWiki (http://pdbwiki.org)

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