Ligand validation in macromolecular structures

P. Kolenko1,2, M. Malý2, T. Skálová1, T. Kovaľ1, J. Dušková1, J. Stránský1,2, L. Švecová1,2, K. Fejfarová1, J. Hašek1, J. Dohnálek1

1Institute of Biotechnology CAS, v.v.i., BIOCEV, Průmyslová 585, Vestec

2Faculty of Nuclear Sciences and Physical Engineering CTU, Břehová 7, Prague

petr.kolenko@fjfi.cvut.cz

Numerous projects of macromolecular structure-function studies involve soaking and/or co-crystallization of ligands. Their presence is afterwards expected to be observed in 2mFo-DFc electron density map and mainly in mFo-DFc (omit) map. However, computation of the electron density map may be distorted by additional factors. In less clear cases (e.g. lower occupancy of the ligand), the initial observed electron density may not contain information on localization of the ligand and further validation procedures are necessary: composite omit map, feature-enhanced map, polder map [1], etc. Current methods are briefly reviewed and their application is shown on a single case of an enzyme:substrate complex.

1. D. Liebschner, P. V. Afonine, N. W. Moriartz, B. K. Poon, O. V. Sobolev, T. C. Terwilliger, P.D. Adams. Acta Crystallogr. D73, (2017) 147-157.

This publication was supported by project BIOCEV (CZ.1.05/1.1.00/02.0109) and CIISB4HEALTH (CZ.02.1.01/0.0/0.0/16_013/0001776) from the ERDF fund and by the Grant Agency of the Czech Technical University in Prague, grant No. SGS16/246/OHK4/3T/14.