I am solving a structure which has a space group P41/P43. I now model a structure into the map and the two protomers wrap along each other like a helix! So it is now clear to be P43.
A problem I face, though, is that each of these protomer should be bound to a peptide ligand. However in the structure the two peptides clash, albeit that when I put only one protomer into the map the ligand fits perfectly fine!
Could anyone suggest why?
Is it possible that each monomeric protein in the solution is bound to exactly 0.5 of the peptide ligand? Can you post a screen shot of the positive difference density for the peptide docked before refinement?
Hi Carter thanks for the reply. I attach below the peptide density in both cases. If only one protomer is modelled, the peptide density fits well at rmsd=1. The extra density there is believed to be from another protomer. However if two protomers are modelled, the peptides twist and basically the density is a mess...
What does the density look like when you have only one peptide ligand modeled with two protomers present? It appears that you posted images of 2 protomers with 2 peptide ligands and one protomer with one peptide ligand... What about 2 protomers with 1 peptide ligand. What I am suggesting is that you may have only one peptide ligand shared between the two protomers in the ASU.
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