Abstract
We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a protein—ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not been described in detail. Here, we present a complete description of the NMR Molecular Replacement implementation as well as several new features that further reduce the time required for structure elucidation.
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taken from the PDB with the protein structure coloured in grey and every non-standard molecule, such as water ions and other organic molecules, coloured in red (PDB 5c5a). b The same protein structure as in (a) ready for the NMR2 structure calculation. The protein chain A was selected and protons were built. The non-standard molecules were removed, the small-molecule of interest was added, coloured in gold, and linked to the protein by “dummy atoms” coloured in blue
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Acknowledgements
We thank the ETH Zürich, who supported this work. Figure 1 includes elements from the free medical images library https://smart.servier.com/ owned by Servier Medical Art and distributed under a creative common license. We thank Overall S. and Greenwald J. for careful reading of the manuscript.
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The ETH Zürich supported this work.
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Orts, J., Riek, R. Protein—ligand structure determination with the NMR molecular replacement tool, NMR2. J Biomol NMR 74, 633–642 (2020). https://doi.org/10.1007/s10858-020-00324-y
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DOI: https://doi.org/10.1007/s10858-020-00324-y