.. _Tertiary_structure:

=======================================
 Identify domains (tertiary structure)
=======================================

- compare to closed conformation

  - load *adk_closed.pdb*
  - select protein
  - *new cartoon*, color differently from the open structure
  - superimpose: Extensions -> Analysis -> RMSD tool: protein

    .. math::

       \mathrm{RMSD} = \sqrt{\frac{1}{N} \sum_{i=1}^N (x_{a,i} - x_{b,i})^2}

    What is the RMSD after superposition?

  - Investigate how the conformation of the molecule changes.

    - Which regions (domains) "move"?

    - Identify two moving domains (called "NMP" and "LID") and one
      constant region ("CORE"):

      - give residue ranges (tip: use Extensions -> Analysis ->
        Sequence Viewer)

      - color regions differently and also mark them in your topology
        diagram
      
   - align on CORE domain only

     What is the final RMSD when aligned on CORE only, i.e. how
     similar are the CORE regions in the two structures?

     What is the overall protein RMSD, assuming that the two
     structures are superimposed on CORE?

.. Solution: domains
.. 
..   * CORE 1-29, 60-121, 160-214
..   * NMP 30-59
..   * LID 122-159
..  Final RMSD when aligned on CORE: 1.97 A, overall 8.0 A