Furthermore and similarly to the structure of the TMD_I, the hydrogen bond network connecting Asp4602.50 of the 455-NLxxxD-460 motif in TM2 with Met6376.48 of the 636-CMxP-639 motif in TM6 is not observed in the modelled structure of the TMD_In.
e, All phi and psi angles in the modelled structure fall within accepted values as determined by Ramachandran analysis with the RAMPAGE server41.
In the modelled structure of C-1, all the interactions between the protein and ATP are well preserved including a correct geometry and bond lengths for the bound metal (Mn2+), which positions the γ phosphate for catalysis.
The solvent accessibilities of the amino acid residues in a 3D modelled structure were calculated using a modification of the Shrake and Rupley method, with a water molecule represented by a 1.4 Å radius sphere.
When the modelled structure of mortalin was subjected to in silico docking with Bcl-2 and Bcl-xL proteins, based on the experimental data and predicted functional residues, mortalin was able to form complexes with Bcl-2 and Bcl-xL.
d, Comparison of the active sites in the crystal structure of AthDHAD and the modelled structure of AstD.
The modelled structure of DdRACK1 features the seven β-propeller architecture with each propeller blade arranged in sequential order and made up of four-stranded antiparallel β-sheets.
The stereochemical quality of the modelled structure was analysed using procheck [36].
In this paper, we explore the interaction between Nse3 and Nse4 and we identify a conserved hydrophobic pocket on the modelled structure of yeast Nse3 which mediates the interaction with Nse4.
