.. _example env 4tvp: Example 8: Closed, PGT122/35O22-Liganded HIV-1 BG505 Env SOSIP.664 Trimer (ligands removed) ------------------------------------------------------------------------------------------- `PDB ID: 4tvp `_ is a structure of the HIV-1 Env ectodomain trimer in a closed conformation, with the PGT122 and 35O22 antibody Fabs bound. This structure has fairly well-resolved glycans, likely because of the stabilization provided by the Fab ligands. Here we prepare a system with just the ectodomain and glycans, omitting the ligands. Many structures in the RCSB are only available in mmCIF format, rather than the older, outdated PDB format; `4tvp `_ is one example. Pestifer uses the native residue indices in the mmCIF file to build the system, not the "auth" indices. .. literalinclude:: ../../../../pestifer/resources/examples/ex08/inputs/hiv-sosip-env-ectodomain2.yaml :language: yaml .. task-table:: ../../../../pestifer/resources/examples/ex08/inputs/hiv-sosip-env-ectodomain2.yaml .. figure:: 4tvp.png :width: 400px :align: center :alt: 4tvp Structure of HIV-1 BG505 SOSIP.664 trimer (PDB ID 4tvp) with Fab ligands deleted from a complete Pestifer build. Glycans are shown in pink stick representation. The run-ready system has approx. 290,000 atoms and is approx. 149 x 197 x 129 Angstroms in size. .. raw:: html

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