5AKM THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MG 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 0.2347
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.40
ligand ACT, MG 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] (313 Kb) [Save to disk]
  • Biological Unit Coordinates (5akm.pdb1.gz) 103 Kb
  • Biological Unit Coordinates (5akm.pdb2.gz) 103 Kb
  • Biological Unit Coordinates (5akm.pdb3.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 5AKM
  • CSU: Contacts of Structural Units for 5AKM
  • Structure Factors (764 Kb)
  • Retrieve 5AKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5AKM from S2C, [Save to disk]
  • Re-refined 5akm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5AKM 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 5AKM
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 5AKM, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5akm_J] [5akm_N] [5akm_F] [5akm_L] [5akm_E] [5akm_K] [5akm_H] [5akm_G] [5akm] [5akm_A] [5akm_D] [5akm_C] [5akm_O] [5akm_M] [5akm_I] [5akm_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5AKM
  • Community annotation for 5AKM at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science