Tom Goddard December 11, 2017
How to look at bound ligands to HSP90 and compare the binding in two structures.
Compare structure determined by class (f20) to similar PDB structures 2xdk and 4lwf which also have ligands with 2 rings joined by a bond. (Chimera 1.12 session.) Found these structures by searching HSP90 bound structures (found 70) and visually inspecting ligand report.
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| Open f20_refine_8-coot-0.pdb Command "color orange ligand & C" menu Tools / Structure Analysis / FindHBond menu Select / Structure / ligand check Only find H-bonds with at least one end selected | RCSB PDB Advanced search HSP90 in title and "bound" in title, 70 hits, Reports: ligands | Commands: open 2xdk matchmaker #0 #1 select #1 & ligand hbond sel cross intermodel false retain true |
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| Commands: open 4lwf matchmaker #0 #2 select #2 & ligand hbond sel cross intermodel false retain true | Show model #0 and #1 (Model Panel) ~ribbon #1 | Movie made in ChimeraX showing 70 bound structures. |