There are a total of around 26 SARS and MERS PL pro crystal structures in the PDB (see Supporting Information Table for the full list), but none from bat coronaviruses. An overlay of the available structures reveals a general conservation of fold in the zinc-binding and catalytic domains, but a flexible linker region between the catalytic and fingers domains results in some differences in the overall shape. In general the SARS structures are slightly more elongated than in MERS (Figure ), and they also display more structural diversity in the ubiquitin-like domain compared to MERS. An initial search of the Protein Data Bank was performed for PLpro templates and these were aligned with Clustal Omega against the full length polyprotein provided for the Wuhan 2019-nCoV (Genbank ID:MN908947), and this produced a 326 amino acid region of interest. Although most of the MERS and SARS PDB hits were of slightly shorter (316-322) length the longer sequence was used as it partially matched two longer Avian Infectious Bronchitis Virus structures. The 326aa sequence was trimmed from the polyprotein and annotated as MN908947_PLpro (Ser1561-Gly1896 polyprotein numbering). At the time of writing there were 17 2019-nCoV polyprotein sequences in the NCBI database, all 100% identical in the PLpro region. Running a BLAST search on the trimmed WH_PLpro.fasta against the full UniProt Knowledgebase indicated that the nCoV PLpro was most closely related (97% identity) to a bat SARS-like coronavirus (UniProtKB:A0A2R3SUX5), followed by another bat coronavirus and a cluster of SARS sequences all at 83% identity (see Supporting Information Table ). Pairwise Emboss-Needle alignments of MN908947_PLpro against individual Bat coronavirus, MERS and SARS sequences (see Supporting Information Figures ), showed that the nCoV PL pro had only 29% sequence identity (48% similarity) to MERS PL pro , 80% identity (88% similarity) to SARS PL pro , but was 97% identical (99% similarity) to a bat coronavirus (UniProtKB: A0A2R3SUX5). A Clustal Omega multiple sequence alignment of MN908947_PLpro against bat A0A2R3SUX5 and representative MERS and SARS PLpro sequences is shown in Figure . This suggested a catalytic triad for the novel coronavirus consisting of Cys114, His275, and Asp289. .*:: : The trimmed MN908947_PLpro sequence was then used for Swissmodel homology model generation. The default Swissmodel template search algorithm initially only suggested 8 high quality SARS templates, 3 of which were semi-redundant as they arise from multiple nonidentical protease monomers in the unit cell. Four of the five crystal structures had ubiquitin bound. In spite of their lower sequence identity, 2 MERS templates were manually added to the template search and the 10 models were built (Table ). Model9 was obtained as a homodimer, although this may be as a result a crystallisation artefact in the template, or a curiosity of the Swissmodel template library. Nevertheless all 10 models were taken through the refinement protocol in Schrödinger Suite 2019, and analysed via manual inspection in Pymol, and semi-quantitatively using Molprobity (See Supporting The refined models were each also analysed by a 100ns molecular dynamics simulation to identify mobile regions and overall model stability. In all cases the ubiquitin-like and zincbinding b-hairpins were the most mobile regions. The presence or absence of a bound allosteric inhibitor did not dramatically influence the mobile regions (Figure ). By contrast, models without an included zinc atom displayed a very high degree of mobility of the four cysteine-containing b-sheets with a downstream effect on the position of the loop bearing catalytic His275, which may be responsible for the observed requirement of zinc for catalytic function of the coronaviral papain-like proteases (see Supporting information Figures S24, S37, S46). 8