PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins

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Further Examples

These examples are shown in the YouTube video:

  • Coronoavirus SARS-CoV-2 spike protein cavity that is a potential drug target
  • Ribosome nascent peptide exit channel
  • Proteasome
  • HIV protease (detailed demonstration of PACUPP commands)
  • Acetylcholinesterase catalytic pocket with inhibitor
  • DNA, major and minor grooves

Some of the above, plus these examples are shown in the slideshow:

  • Orthogonal tunnels accessing the heme in protoglobin
  • Oligopeptide-binding protein A with an octapeptide in a buried cavity (detailed demonstration of PACUPP commands)

The PACUPP website adds:

  • Lysozyme with inhibitor in catalytic cleft

Sample PACUPP Output PDB File

The PDB file written by PACUPP and used in the above scenes can be downloaded. PACUPP commands will not be available unless you download PACUPP and drop this PDB file into the Jmol.jar application started from within that download.

See Also

References and Notes

  1. Liu QP, Sulzenbacher G, Yuan H, Bennett EP, Pietz G, Saunders K, Spence J, Nudelman E, Levery SB, White T, Neveu JM, Lane WS, Bourne Y, Olsson ML, Henrissat B, Clausen H. Bacterial glycosidases for the production of universal red blood cells. Nat Biotechnol. 2007 Apr;25(4):454-64. Epub 2007 Apr 1. PMID:17401360 doi:10.1038/nbt1298
  2. With very fine cavity detail, PACUPP identifies 63 distinct cavities. 30 have a single pseudoatom each, and 20 have 2-4 pseudoatoms each. By default, PACUPP hides cavities with <5 pseudoatoms.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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