The secondary structure looks like this, the clover leaf. The amino acid is bound at the top, the anticodon at the bottom. The lines represent the base pairing.
For the 3D structure you have to first consider that helices are formed with base pairing - twist around all those parts. In tRNA there is an important tertiary element, the connection between the left and right loop - fold the molecule. You will get something like this.
The open end is shown in read, the anticodon green, the right loop yellow, the left loop cyan.
Twisted around:
The open end:
The anticodon loop:
These three bases are probably the anticodon. They are GAA which correctly codes for Phe which this piece of tRNA is supposed to do.
If you want to move the molecule yourself you can find the link to a jmol applet from the pdb.
2 comments:
I'm glad to see some nice molecule images again. In fact lately I've missed them a bit ];)
Anyway. The surface near the anticodon loop and also some other parts of the tRNA molecule look unnatural(parted). This is because by default atoms with "HETATM" id in the PDB file are not included in the surface drawn by Pymol. Try forcing them with this:
set surface_mode,1
yes, I forgot that drawing molecules is pretty fun :)
thanks, I was wondering why there were these empty areas
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