B-RAFWT. A) The conformation of B-RAFWT after 15 ns of simulation time. The different structural elements in the protein are coloured according to the structure method in VMD and the names of the sub-structures are shown. The A-loop contains 30 residues and is in the space between the P-loop, the αC-helix, the β6-strand, the F-loop and the αG-helix (see text for details). B) A close look at the conformation of the major catalytic residues and the identified hydrogen bond network in the unbounded B-RAFWT after 15 ns of simulation time (The position of Gly596 is shown in Figure 7). The dotted lines and the adjacent numerical values represent the H-bonds and their distances.
Fratev and Jónsdóttir BMC Structural Biology 2009 9:47 doi:10.1186/1472-6807-9-47