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Fig. 8 | Virology Journal

Fig. 8

From: Study of SV40 large T antigen nucleotide specificity for DNA unwinding

Fig. 8

Structural implications of LT nucleotide specificity. a Residues cP427, cF547, and cP549 (orange) are presented in sticks to demonstrate the rigidity in the spatial arrangement surrounding cS430 (magenta). b The charge-charge interaction between tK419 (magenta) and the -OH group on the sugar molecule of TTP. c The unique hydrophobic lining of nine hydrophobic residues (green), including cW393 and cL557 around base of the bound nucleotide in the nucleotide pocket of LT. d The function of the hydrophobic lining through an induced fit mechanism as illustrated with TTP, in which cW393, cL557 and other hydrophobic residues alter their conformations compared to those in panel-C. TTP and UTP were docked and fitted into the LT nucleotide binding pocket utilizing AutoDock Vina in PyMol. The lowest energy state docking with the correct alignment of the α-β-γ phosphates of the bound NTP was chosen for their respective panels

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