PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins

This page is under construction. Eric Martz 23:26, 11 December 2020 (UTC)

PACUPP is an open-source free program for identifying and visualizing cavities in macromolecules. It is a Jmol script that fills pockets, cavities, tunnels/channels in proteins with pseudoatoms. PACUPP provides tools to isolate cavities of interest and display their contents, their linings (and list the lining atoms, spreadsheet-ready), entrances (mouths), volumes, shapes, and dimensions.

PACUPP adds the pseudoatoms (holmium, Ho, think "holes") to an output PDB file, which can then be viewed in Jmol with PACUPP commands, or in the software of your choice (e.g. PyMOL, Chimera, VMD, Cn3D, etc.). PACUPP (Jmol) is Java-based, and thus works in Windows, macOS, and linux.

PACUPP Version 1.0 was released December 9, 2020.

The PACUPP program and documentation can be downloaded at molviz.org/pacupp. There you will also find a YouTube Video demonstrating how to use PACUPP with several examples, and a slideshow also providing examples and some guidance in how to use the program.

Example

At right is a (alpha-N-acetylgalactosaminidase) 2ixb^[1]. It has a channel containing NAD, and a pocket where substrate can access the catalytic site, which includes the NAD.

With default settings (cavity detail: fine; cavity size: small), the two entrances to the channel containing NAD are not quite connected. With cavity detail set to very fine, the channel connects. having 5 or more pseudoatoms/cavity^[2]. All but one of these are shallow pockets on the surface. In contrast, the pink cavity penetrates into the protein.

This is easier to see when the (PACUPP command d; also the backbone trace was toggled off with the command b). Only the formerly pink (largest) cavity has blue (deep) pseudoatoms. In PACUPP, .

ReferenceReference

↑ 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
↑ 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.

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Eric Martz

[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

[cavall-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.

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