3
$\begingroup$

I'm looking at the structure of this protein, which I beleive is supposed to be a single polypeptide chain, since on the PDB page it says:

Unique protein chains: 1

But using the 3D viewer, there seem to be a few "loose ends" i.e. it looks like the protein is composed of multiple polypeptide chains.

This is was I see - you can see a separate chain there at the bottom.

Where am I going wrong here?

$\endgroup$
5
$\begingroup$

Some parts a the protein are a bit more flexible, also in the protein crystal. These parts don't give clear electron density after x-ray diffraction, and are removed from the resulting model structure. Often the N- and C-terminal ends are removed, this is something you'll find in many .pdb structures, but sometimes also loops are removed, resulting in two extra loose ends.

The authors were nice to note in the comments section of the pdb file exactly which residues were removed from the model (#465).

There might be tools available to model loops into the structure so you'll have one continuous chain in the .pdb file, but I really don't know which one is best (of course they're all completely unreliable).

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.