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Do they form a peptide bond? Or is it just some affinity/van der Waals interaction?

Is the mechanism enzyme catalized?

Are the residues/moieties at the join site known? Could they be introduced to synthesized peptide fragments to achieve something like native chemical ligation?

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    $\begingroup$ Exteins are joined; Inteins are removed and van der Waals interactions are non-bonding interactions and it is definitely not the case. Can you narrow down your post to a specific issue (perhaps the last one as it seems non-trivial) but you have to add more details. $\endgroup$ – WYSIWYG Aug 13 '15 at 10:08
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    $\begingroup$ I really mean the joining of the split inteins, which in my understanding must happen before the whole intein (consisting of 2 split intein parts) can be removed. en.wikipedia.org/wiki/Intein#Split_inteins $\endgroup$ – Reto Höhener Aug 13 '15 at 21:34

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