Question: Why Residues are Missing In This Protein Structure?
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gravatar for gmgmsiva
6.3 years ago by
gmgmsiva10
United States
gmgmsiva10 wrote:

when i am open my protein(eg-1cqe) in swiiss pdb viewer ,it show some aminoacids side chains are missing..why?1cqe is a complete reference protein.

structure protein • 3.8k views
ADD COMMENTlink modified 5.1 years ago • written 6.3 years ago by gmgmsiva10

Maybe parts are flopping around. You won't see them in a structure then.

ADD REPLYlink written 6.3 years ago by Devon Ryan95k

You'll get better answers if you use more informative question titles and tags. In this case: "why are residues missing in this protein structure?" and "protein, crystallography, structure" would be good. Fixing that for you now...

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Neilfws48k

Are you sure that the amino acids are in the pdb file?

ADD REPLYlink written 6.2 years ago by sentausa640

The original question could have been rephrased as why not all residues in a protein were contained in its structure, so no, they weren't in the structure. See my comment above and Nielfws' reply below.

ADD REPLYlink written 6.2 years ago by Devon Ryan95k
2
gravatar for Neilfws
6.3 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Not sure what you mean by "complete reference protein" - presumably you mean that a corresponding sequence record (e.g. in UniProt) is annotated as "complete"?

However: to expand on the comment by dpryan79. It is not uncommon for residues to be missing from protein structures. This happens when regions of protein molecules in the protein crystal are disordered, mobile or "floppy" and so do not generate an interpretable X-ray diffraction pattern.

Here is an introduction to protein crystallography which explains this and other issues; there are many others on the Web.

ADD COMMENTlink written 6.3 years ago by Neilfws48k
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