The example that we will consider is taken from a study which investigated the reaction mechanism of cAMP-dependent protein kinase using a mixture of QC, MM and QC/MM approaches. The reference may be found here. The enzyme is commonly referred to as PKA and it catalyzes the transfer of a phosphoryl group from adenosine triphosphate (ATP) to the serine sidechain of a target peptide or protein.
There are many criteria for selecting a structure for simulation but some relevant ones are:
There will rarely be a single PDB structure that is "ideal" for a particular simulation study. Instead, it is often necessary to carry out a detailed comparison of several structures before a choice can be made. It is also common to employ multiple structures, either to construct a "hybrid" structure that conforms better to the system that is to be simulated than any of the experimental structures, or so that the results of simulations with different structures can be compared.
The structure chosen for this study was pig cAMP-dependent protein kinase with PDB entry 1CDK. It can be visualized using a wide-range of programs, some of which are indicated here. The structure is of reasonable resolution (2.0 Å) and, importantly, has ligands bound in the active site that resemble very closely those that are involved in the catalytic reaction. These include: two Mn2+ ions, as opposed to Mg2+ ions; an inactive twenty-residue peptide substrate in which the active serine is replaced by an alanine; and a 5'-adenyly-imido-triphosphate molecule that is very similar to ATP.