Sybyl version 8

All protein structures and ligands were processed by using the software Sybyl, version 8.1 (Certara USA, Princeton, NJ, USA). All atoms were checked for atom- and bond-type assignments. Amino- and carboxyl-terminal groups were set as protonated and deprotonated, respectively. Hydrogen atoms were computationally added to the protein and energy-minimized using the Powell algorithm with a coverage gradient of ≤0.5 kcal (mol·Å)⁻¹ and a maximum of 1500 cycles.

The crystallographic structure of the enzyme beta laccase from Trametes versicolor (PDB code 1KYA [16 (link)]) was the template for the homology modeling of gamma and delta isoforms. The Modeller software, version 9.14 (copyright © 1989-2016 Andrej Sali; maintained by Ben Webb at the Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, Mission Bay Byers Hall, University of California San Francisco, San Francisco, CA, USA) was used [41 (link)]. The D206A beta isoform model was obtained by manually editing the wild type structure with the software Sybyl, version 8.1 (Certara USA, Princeton, NJ, USA). For sequence analysis, a local pairwise alignment was conducted by using the on-line tool EMBOSS-Water Pairwise Sequence Alignment (EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK; http://www.ebi.ac.uk) and the Smith–Waterman algorithm was chosen.