Homology modeling approach was taken for determining the tertiary structure of the hypothetical protein. Swiss Model server predicted the 3D structure (Fig. ) based on the most favored template 4zlh.1.B (PDB ID: 4ZLH_B). 4ZLH is the crystal structure of Escherichia coli protein with lipopolysaccharide assembly protein B (LapB) cytoplasmic domain. This template protein is a homodimer which has two chains (Chain A and Chain B) and chain B was used to build the model by Swiss Model server. For this template, values of Global Model Quality Estimation (GMQE), Quaternary Structure Quality Estimation (QSQE) and identity score were 0.83, 0.51 and 76.04, respectively. The quality of the model was assessed by PROCHECK through Ramachandran plot analysis, where the distribution of ψ angle and the φ angle in the model within the limits are shown (Fig. , Table ). Residues in the most favored regions covered 93.1% which indicated good quality and validity of the model. Verify3D showed 94.69% of the residues have averaged 3D-1D score ≥ 0.2 (Fig. ), which indicates good quality of the environmental profile for the predicted model. The overall quality factor predicted by ERRAT server was 98.752, which validates the model as a good one. Similarly, Phyre2 server predicted the 3D model with 100% confidence and 87% coverage. 337 residues out of 389 were modeled with 100% confidence by the single highest scoring template which was c4zlhB (PDB ID: 4ZLH_B). PROCHECK predicted 91.0% residues in the most favored regions, which indicates good confidence for the predicted model (Table ). 87.33% of the residues had averaged 3D-1D score ≥ 0.2, according to Verify3D which validates the predicted model. ERRAT server quality factor score was 89.6024, which is suggestive of a good valid model. The tertiary structure modeled by Swiss Model was more preferable than the model predicted by Phyre2 server considering Ramachandran map analysis, Verify3D results and ERRAT server results. Therefore, energy minimization was performed using YASARA server for the Swiss Model 3D structure and scene file (.sce) was visualized in YASARA scene. The energy calculated before energy minimization was -338180.6 kJ/mol and that was changed to a far less value of -431656.0 kJ/mol after energy minimization which makes the predicted model more stable.