Dear all,
I require some guidance with a modelling problem I am having. I am attempting to model a short 11 residue sequence around a template taken from the small molecule database:
ATOM 1 SG CYS A 1 4.774 5.927 9.587 1.00 0.00 ATOM 2 CB CYS A 1 4.175 7.673 9.917 1.00 0.00 ATOM 3 SG CYS A 2 5.091 3.544 6.534 1.00 0.00 ATOM 4 CB CYS A 2 6.560 3.252 7.614 1.00 0.00 ATOM 5 SG CYS A 3 1.160 3.172 6.513 1.00 0.00 ATOM 6 CB CYS A 3 0.028 2.178 7.542 1.00 0.00 ATOM 7 SG CYS A 4 0.936 5.818 9.617 1.00 0.00 ATOM 8 CB CYS A 4 -0.419 4.795 10.238 1.00 0.00 ATOM 9 SG CYS A 5 2.942 2.405 9.819 1.00 0.00 ATOM 10 CB CYS A 5 4.547 1.918 10.664 1.00 0.00 ATOM 11 SG CYS A 6 2.713 6.590 6.171 1.00 0.00 ATOM 12 CB CYS A 6 2.800 5.754 4.601 1.00 0.00 HETATM 13 CU CU1 A 7 2.896 4.649 9.731 1.00 0.00 HETATM 14 CU CU1 A 8 4.201 5.454 7.463 1.00 0.00 HETATM 15 CU CU1 A 9 3.182 2.965 7.621 1.00 0.00 HETATM 16 CU CU1 A 10 1.497 5.188 7.518 1.00 0.00 END
I require the first 4 CYS residues of the template structure to align with 4 CYS residues from my query sequence (as shown in the following alignment), and for the orientation of these residues around the copper cluster to be maintained
>P1;TemplateTest Structure:templatetest:1:A:10: : : : : C-C-----C-CCC....* >P1;Ace1 Sequence:Ace1: : : : : : : : CRCDEGEPCKC--....*
I have performed an unrestrained alignment that produced a model, but was unable to keep the CYS residues in the correct orientation and moved the polypeptide 80A away from the copper cluster!
Attempts to restrain the system, by putting distance restraints between the SG atoms of the CYS residues and coppers have been unsuccessful. The following is an example of the commands I have been trying as a distance restraint.
rsr.add(forms.upper_bound(group=physical.xy_distance, feature=features.distance(at['CU:7:A'], at['SG:1']), mean=2.28, stdev=0.01))
Any guidance that could be given on this problem would be much appreciated!
Regards
Stephen Hearnshaw