Ligands

• Download 1AKE from the PDB (or use 1ake.pdb from the course directory)
• show protein chain A
• show the co-crystallized ligand Ap5 (resname AP5")
  • resname AP5, licorice, color: name
• show charged residues within 5 Å of the ligand
  • same residue as (charged and within 5 of resname AP5)
  • use representation licorice, color: name for the residues, make ligand VDW.
  • Which side chains make contact with the ligand?
  • What have they got in common? (Tip: try out color: restype)
• water
  • show crystal water oxygens as VDW or licorice (small spheres)