The mutation and resultant adaptability of HIV-1 reverse transcriptase (RT) present a major challenge to the design of the effective antiviral strategies because many initially potent drugs lose efficacy over time. Even though there is an urgent need for a comprehensive understanding of the molecular mechanism of anti-HIV drug resistance by mutant RTs, the unavailability of the structural information of the mutant RTs has prevented detailed investigations. In this study, the active site of the 3TC-resistant (M184V) RT is constructed by a computational method, which clearly shows that the side chain of Val184 occupies the binding site for the nucleoside triphosphates. Therefore, the distance between the side chain of Val184 and the sugar moiety of the nucleoside triphosphate must be closely related to the cross-resistance by M184V RT. The natural substrates, 2′-deoxyribo nucleoside triphosphates, escape from the steric stress from the bulky side chain of Val184 by virtue of the d-sugar conformation as well as the interaction of its 3′-OH group with Tyr115, which locates the nucleoside triphosphate out of the clashing distance from Val184. Similarly, the energy-minimized structures of various d-dioxolane nucleoside triphosphates (TP)/RT complexes indicate that the d-dioxolane sugar moiety acquires enough distance from Val184 due to the specific interaction of its 3′-oxygen atom with the nearby enzyme residues such as Tyr115 and Arg72.