.. -*- encoding: utf-8 -*-

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)
  

.. _1AKE: http://dx.doi.org/10.2210/pdb1ake/pdb