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If I've got the site right (the equivalent to Asn833 in your image would be Asn858 in 3rjo?) then the first thing I'd be checking is if you have an unmodelled tail or loop that could be interacting here across a symmetry interface. The dramatic kink in the helix there looks like an asparagine, glutamine or serine sidechain could stably H-bond to the backbone in a conformation reasonably consistent with that three-pronged density. You also have partially-unmodelled lysine residues at the 834 and 831 positions, and quite a few other positive residues in the vicinity. I'd be looking for candidates with negative charge. Could the spheroidal blob near Asn833 be a sulfate bridging it and Lys834? On 2017-08-18 22:17, Maben, Zachary wrote: > Hello, > > I am refining a few datasets of my protein of interest (ERAP1) bound > to various inhibitors, and I repeatedly observe a positive density > peak near an asparagine. I first thought this might be a glycan, but > this site does not fit the canonical N-linked glycosylation motif > (this site sequence is NKL). Previous crystal structures of this > protein do not identify any ligand at this position. > > https://www.dropbox.com/sh/2wdax5uqlb1f4m3/AABQlGK2_mgibtqnm61E-7o0a?dl=0 > [1] > > [1] > > Asn833 positive density [1] > www.dropbox.com > Shared with Dropbox > > I would appreciate any suggestions of what this density might be. > Thank you for your help. > > Best, > > Zach Maben > > Stern Lab > > Pathology Department > > University of Massachusetts Medical School > > [1] > > > Links: > ------ > [1] > https://www.dropbox.com/sh/2wdax5uqlb1f4m3/AABQlGK2_mgibtqnm61E-7o0a?dl=0