The whole protein looks like this, the ligand is shown in red.
If you draw the protein with its van der Waals surface, you notice that there is a small opening which is probably the place where the ligand entered the binding pocket.
Apparently the receptor closed again and the molecule is trapped in there.
If you eat away some of the outer amino acids, you can take a better look at the binding pocket.
Or at a semi transparent binding pocket:
Remove some more amino acids that are in the way and it'll look like this.
How do you create those picutres in pymol?
First you select one chain (the fact that there are four chains is just because that's how it crystallizes):
select cha, chain aIf you go for "preset pretty", you can see the ligand and select it. Call it lig. Then you can modify it, give it double bonds, show it as ball and stick model, ...
For the main protein you may want to select the different secondary structures:
select helix, ss h and cha2
select sheet, ss s and cha2
select loop, cha2 and not (ss h or ss s)Then you can color those the way you want.
If you want a surface, it makes sense to duplicate that chain a and show the duplicate as a surface.
If you want to select the binding pocket, go for:
select pocket, (lig around 5)Then you can erase some of the amino acids that are in the way.
Of course after doing all this, you have to play around with colors, perspectives and rendering methods.
9 comments:
"you notice that there is a small opening which is probably the place where the ligand entered the binding pocket."
You've been seduced by the beauty and staticness of the crystal structure. When Kendrew first solved sperm myoglobin 50 years ago, they noted that there seemed to be no way for oxygen to get inside to bind to the iron contained in the porphyrin ring. The molecule had to breathe (e.g. change conformations).
Almost certainly the glucocorticoid receptor must as well, in addition to further changing its shape once the ligand is bound to it and the receptor begins to cooperate with other proteins (cofactors) and the megaDalton RNA polymerase II complex to turn on the gene downstream from its binding site on DNA.
Retread
yes, I did not mean to say that the molecule slipped through this small hole. but I think it is very interesting how it is caught in there
Did you calculate a partial surface for the binding pocket or just moved the slab around?
this was just the surface of the protein without ligand, I did not calculate anything
I don't understand what you mean by slab
I was wondering how did you do the last two images. By "slab" I mean moving the two clipping planes. You can move them ether by the clip command or by scrolling the mouse wheel and holding Shift/Ctrl(Strg)/Shift+Ctrl keys. That's easy to work with, but some times it's hard to remove all the obstacles without hiding parts of the ligand.
I know there's a way for showing in pymol only a partial surface like on this image. After some searching I've found how to do that on the PyMolWiki. I was just curious if you did it this way or had some experience with this method.
oh, I understand. I did two things, one was "slabbing". actually I did not know that Ctrl+MouseWheel command, so I zoomed on the ligand and then just used the mouse wheel
but there were things in the way. So I duplicated the protein and erased part of it, just by clicking on the amino acids and removing them. then I showed the original protein as cartoon and the duplicated protein as surface
aside from this figure I have never done it like this but I think manually erasing things that are in the way is the easiest thing, probably not the fastest though
Wow, it's really gorgeous. Thanks.
Polly
sure, I am glad that you like it
I would like to thank you for putting my mind in motion. The partial surface thing couldn't let me sleep for a long time... but then I came up with some ideas.
I think this could be of some interest to you.
Regards
Dawid
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