.. -*- coding: utf-8 -*-

.. |->| replace:: →

=========
 Summary
=========

AdK secondary and tertiary structure
====================================

AdK is a dynamic enzyme, which can undergo a large conformational
change between an open and a closed conformation. The backbone RMSD
between the two conformations is about 7.16 Å.

AdK contains a central beta sheet (with strands A1 to A5) between four
helices (H1, H5, H7, H8), making up the CORE domain (residues 1-29,
60-121, 160-214). This CORE domain does not change much between the
open and closed conformation (RMSD 1.97 Å of CORE).

The NMP domain, consisting of helices H2—H4 (residues 30-59), and the
LID domain (H6 and two small beta sheets B1/B2 and C1/C2/C3, resids
122-159) are very mobile. On closing, they both fold towards CORE on
hinges. When RMS-fitted on CORE, the overall RMSD is 8.0 Å.

.. figure:: /images/adk-topolo.*

   Topology diagram of AdK.


AdK Ligand
==========

The AP5 ligand mimics the transition state of the phospho-transfer
reaction. Phosphates are negatively charged, hence only basic
(positively charged, blue) residues are in contact.

.. image:: /images/1ake_ap5.jpg

.. image:: /images/ap5_chargedres.jpg