Fig. 2.

Homology model and Quality metrics of AhR LBD. a Modelled structure of mouse AhR LBD with helices are shown in red, sheets are shown in yellow and loops are shown in green color. The figure indicates the vicinity of the α1-helix to the N-terminus. b Superimposition of the template (light blue) with the mouse AhR LBD model (light brown) in cartoon secondary structure with an RMSD 1.02 Å using CLICK server. c Ramachandran plot showing energetically allowed regions for backbone dihedral angles ψ against ϕ of amino acid residues in modelled mouse AhR LBD protein structure. The plot of AhR LBD model shows 97.6% residues in favored region, 2.4% residues in allowed region and 0.0% residues in outlier region from the total residues. d Represents the ProSA analyses of the generated mouse AhR LBD structure model. The calculated quality (Z) scores (closed circles) are displayed in the context of all experimentally determined protein structures available in the Protein Data Bank with each dot representing a distinct structure solved by X-ray crystallography (light blue) or NMR (dark blue). The Left side of the figure represents the prosa-web plot of template 4M4X chain A with a z-score value of − 3.86 whereas the right side of the figure represents the prosa-web plot of built AhR LDB model with a z-score value of − 1.37