BACKGROUND: Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common. RESULTS: Here, we analyze the long channels (i.e. >15 Å) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 Å. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein. CONCLUSIONS: The majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate.

Department of Physical Chemistry Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Olomouc tř 17 listopadu 12 Olomouc 771 46 Czech Republic

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK

Faculty of Informatics Masaryk University Brno Botanická 68a Brno 602 00 Czech Republic

National Centre for Biomolecular Research Faculty of Science and CEITEC Central European Institute of Technology Masaryk University Brno Kamenice 5 Brno Bohunice 625 00 Czech Republic

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Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes

ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

ChannelsDB: database of biomacromolecular tunnels and pores