Fig. 5

Three-dimensional structure of type II L-asparaginase from Chryseomicrobium amylolyticum through different modelling servers and their validation. (A): 3D monomer structure through the ‘iTASSER server’; (B): Ramachandran plot-based validation of the ‘iTASSER’ based structure; (C): ProSA-based quality evaluation ‘iTASSER’ model; (D): ProSA estimated energy profile of the ‘iTASSER’ model; (E): 3D monomer structure through the ‘Alphafold’; (F): Ramachandran plot-based validation of the ‘Alphafold’ based structure; (G): ProSA-based quality evaluation of the ‘Alphafold’ model. (H): ProSA estimated energy profile of the ‘Alphafold’ model; (I): 3D structure of the tetramer through the ‘Alphafold’; (J): Ramachandran plot-based validation of the tetrameric structure through the ‘Alphafold’; (K): ProSA-based quality evaluation of the ‘Alphafold’ tetramer structure; (L): ProSA estimated energy profile of the ‘Alphafold’ tetramer structure. In (B, F and J) figures, the alphabets, (A, B, and L) designate amino acids in favored regions; a, b, l, and p designate amino acids in additional allowed regions; ~a, ~b, ~l, ~p designate amino acids in generously allowed regions. The red color shows the most favored regions. In (C, G, and K) figures, ProSA-web z-scores of all protein chains in PDB identified by X-ray crystallography (light blue) or NMR spectroscopy (dark blue) are depicted. The z-scores of the studied protein are represented by a black dot. In D, H and L: ProSA analysis showed that the knowledge-based energy values of most of the amino acid residues are negative, indicating the reliability and quality of the built 3-D structures.