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. Author manuscript; available in PMC: 2013 May 8.
Published in final edited form as: J Chem Theory Comput. 2012 Mar 15;8(5):1750–1764. doi: 10.1021/ct200680g

Fig. 3.

Fig. 3

Illustration of the Cα -distance restraints (B – D; the parts mostly blue-colored corresponding to NBD-I and those mostly green-colored corresponding to NBD-II) imposed on the nucleotide-binding domain (A) of DnaK from E. coli (PDB code: 2KHO). (B) The RI-RII restraint system in which only NBD-I (from I4 to E171) and NBD-II (from G186 to N366), excluding the boundary residues, are restrained to their conformations in the 2KHO structure. (C) The RI-II restraint system in which the whole NBD (from I4 to N366) excluding its C-terminal region is restrained to its conformation in 2KHO. (D) The RI-II-small restraint system in which the whole NBD is restrained to the putative ATP-bound conformation (with NBD closed), obtained with MODELLER41 using 3C7N:A as template. It should be noted that the distance restraints (from the 2KHO structure) between RI and RII were also imposed on SBD-β (from V394 to S505), not shown in this Figure.