I wanted the whole protein structure of beclin-1 protein, but since I could not find he whole protein structure on it's own, I went for the structure of PI3KC3-C1 complex, which included the whole Beclin-1 protein (pdb id: 8sor).
But when I opened the protein in Autodock, I found that certain amino acids are missing from the beclin-1 structure. Please provide me with suggestions on how to tackle this problem.
Thank you.
You can get a model of the full-length protein from AlphaFold: https://alphafold.ebi.ac.uk/entry/Q8NEB9. Comparing the different available experimental structures (red) against this model (yellow), you can see that besides the N- and C-termini not being resolved in the structures, there is a large loop (ca. res 410-470) that is not resolved, although some structures show fragments of it (blue). The relative orientation of the two folded domains as well as the conformation of the linker between them depends on the other components of the complex and would most likely be flexible in the isolated component. How to best prepare the molecule for docking depends on the questions you wish to answer. I would use the best resolved structures of the individual domains as templates and fill in the minor gaps using homology modelling. If you are docking small molecules, you can dock to the individual domains. The large loop is most probably unstructured and cannot be modelled with confidence - you can either leave a gap or replace it with a minimal loop to connect the loose ends - again depending on the exact pupose of your model.
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