.. _example env 7txd: Example 11: Open, Symmetric D9/CD4-liganded HIV-1 SOSIP Env Ectodomain Trimer (ligands removed) ----------------------------------------------------------------------------------------------- `PDB ID 7txd `_ is a structure of the HIV-1 Env BG505 SOSIP-664 ectodomain trimer in an open conformation, with the two-domain soluble CD4 construct (sCD4) and 17b Fab fragment bound. This structure is missing the so-called V1/2 loop between residues 100 and 162 on each gp120. Here, we substitute that span of residues with a literal triglycine (Gly-Gly-Gly) sequence--this ensures psfgen doesn't just pop standard N- and C-terminal patches across that gap. This is an alternative to what we did in :ref:`4zmj `, where we opted to build in missing residues following sequence. We also model in residues missing from gp41's and fold them into alpha-helices. The ligands are removed from the structure, and the system is solvated in a water box. .. literalinclude:: ../../../../pestifer/resources/examples/ex11/inputs/hiv-sosip-env-ectodomain3.yaml :language: yaml .. task-table:: ../../../../pestifer/resources/examples/ex11/inputs/hiv-sosip-env-ectodomain3.yaml .. raw:: html

Example author: Cameron F. Abrams     Contact: cfa22@drexel.edu