Hello, buds
I need your help to interpret the attached data.
R group in serine is CH2OH, but the data show the two O in the group with hydrogen bonds with a molecule. Is this correct? Possible?
Please give comments. Thanks a lot for your help.
Hope in safe amid COVID-19.
The entity you labelled SER in not a valid amino acid - the two oxygens would indicate a glutamate or aspartate side chain, but when you would expect the carboxylate group and adjacent CH2 carbon to be planar, and for an apartate you would expect one CH2, for a glutamate two CH2s between the carboxylate and the backbone. Are you using a strange abstraction of the side chain where you represent the Calpha-Cbeta-Cgamma by a single straight line? If your blue lines are supposed to represent hydrogen bond, it is anyhow wrong, as the hydrogen in the putative tyrosine in the top right corner is pointing away from the hydrogen bond acceptor oxygens in the putative aspartate - you would have to rotate around the bond between the aromatic ring and the OH in the residue to get the hydrogen to point towards one of the aspartate oxygen.
Thanks for your comment (@ Annemarie Honegger)
My idea is the same as yours. I think that is impossible. Calpha at SER makes a peptide bond with the amino group of another amino acid. The branch on SER at the above figure must be an R group (CH2OH), I think. I could not understand why SER showed two oxygens there. That is a computational error? I need to rerun and recheck the docking assay. And then, I want to talk the data with you.
Thanks a lot for your help. Hope you are in safe.
I actually think that is really weird (@ Annemarie Honegger) .
SER280 has two oxygens (actually that is impossible, I could show a different binding mode) and SER287 shows one oxygen in the R group (that is a common mode). Do you think that is a computational error?
First of all, use a less abstracted visualisation - it will be easier to see what is happening in an all-atom representation. In your image, I cannot really tell whether the problems I see are due to the way you depict your structure, or to the structure itself. Can you send me the structure file itself? Which program are you using to create the image? If the labelled residue actually is a serine, you might have an alternative localisation for the OH group in your structure file (both side chain rotamers being significantly populated in the crystal). If this is the case, you would have to resolve the issue and decide on the rotamer you want to use before docking.
Yes, my final thinking is a rotamer of serine, but that is possible? I'm not sure. I send you a pdb file. It shows the exact SER280.
I see. If you open the pdb file in a text editor, and scroll down to Ser 280, you find the following:
ATOM 676 N SER A 280 8.963 12.229 0.233 1.00 0.00 N ATOM 677 CA SER A 280 9.435 10.853 0.148 1.00 0.00 C ATOM 678 CA SER A 280 9.440 10.855 0.152 1.00 0.00 C ATOM 679 C SER A 280 8.651 10.071 -0.871 1.00 0.00 C ATOM 680 O SER A 280 7.632 10.566 -1.422 1.00 0.00 O ATOM 681 CB SER A 280 9.264 10.168 1.498 1.00 0.00 C ATOM 682 CB SER A 280 9.287 10.172 1.510 1.00 0.00 C ATOM 683 OG SER A 280 7.890 10.077 1.838 1.00 0.00 O ATOM 684 OG SER A 280 9.902 10.899 2.563 1.00 0.00 O
CA, CB and OG have double entries - but they lack the altLoc character in column 17 (just before the amino acid name) (see https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html for a description of the pdb atom record format).
Look at the corresponding section in your original protein structure - I would expect that the duplicated atoms carry an "A" and "B" in this position. "A" would be the most highly populated rotamer. This is not due to your docking (although the docking program you use apparently is not able to resolve this issue), but it is a problem in the original file. You have to either remove the alternative localization , or use an alternative starting structure that does not have this problem.
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