aGPCR

Question

[keyajoshi1996]

I need to find out the rmsd of my reference structure with all the intracellular residues in the TM6 domain. I am not sure how to find out these residues.

https://gpcrdb.org/structure/homology_models/agrg1_human_active

https://gpcrdb.org/protein/agrg1_human/

Answer 1

[Mensur Dlakic]

TM6 is not a domain, it is a helix. In the second link you posted, all trans-membrane helices are shaded in light blue, and labeled TM[1-7]. Then you have extracellular loops (ECL[1-3]) and intracellular loops (ICL[1-3]). The residues you want most likely are PHTQ in ICL3 that precedes TM6.

Answer 2

[keyajoshi1996]

Thank you so much for your help. I wanted to ask you one more question, if you can please help me with that. How to determine what all residues are present in the extracellular site of ECL-2 loop region.

https://gpcrdb.org/protein/agrg1_human/

https://gpcrdb.org/structure/homology_models/agrg1_human_active

[Mensur Dlakic]

You can do this as well as I can. Look for all the residues that are not shaded in light blue (those are TM helices) and are labeled ECL2. That is a long loop, almost 30 residues.

[keyajoshi1996]

Thank you so much for all the help.