Thank you Elaine. The problem is that the AlfaFold structures are devoid of side chains. Is there a way to get round this problem? Have a good day George
On 9 Jul 2023, at 17:29, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, The approach that you described is the same that I would try. Hopefully the cysteine will be in the right place. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2023, at 3:33 AM, George Tzotzos via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
I’d be grateful for any suggestions regarding the following problem/question.
Problem Placing of the haem-iron centre in mosquito P450 structure(s) obtained by means of AlfaFold. This is required for follow up docking simulations. There no insect P450 structures deposited in PDB. However, there are numerous mammalian P450 crystal structures some of which are homologous to the mosquito structures I’m dealing with. A distinctive feature of these structures is a haem-iron centre tethered to the protein via a cysteine thiolate ligand. Six regions have been designated as substrate recognition sites (SRS 1-6) based on comparative sequence analysis methods. These SRS are conserved and are thought to participate in the formation of the substrate access channel, and form part of the catalytic site surrounding the haem iron center.
My initial approach would be to use Chimera to align the AlfaFold structure against its mammalian homologue PDB structure and assume that the haem-iron centre would be located in the same place.
Is there a better way to achieve the same objective?.
Your help will be greatly appreciated.
Best regards
George