Sandbox Reserved 1440: Difference between revisions
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In the 6B1E protein with resolution 1.77 Å, the big density sizes are far from the ligand, which doesn’t have a significant impact on the binding pocket interaction. All of the missing electron density is not impacting the actual validity of the binding site. | In the 6B1E protein with resolution 1.77 Å, the big density sizes are far from the ligand, which doesn’t have a significant impact on the binding pocket interaction. All of the missing electron density is not impacting the actual validity of the binding site. | ||
Figure 1g: | Figure 1g: | ||
http://proteopedia.org/wiki/images/7/7a/6b1e.png | |||
In the 6B1E crystal structure, the catalytic triad seem to have some missing density but still not significant enough to be an invalid structure and interaction with the LF7 ligand. | In the 6B1E crystal structure, the catalytic triad seem to have some missing density but still not significant enough to be an invalid structure and interaction with the LF7 ligand. | ||
Figure 1h: | Figure 1h: | ||
http://proteopedia.org/wiki/images/6/6e/6b1e_density.png | |||
== 4N8D == | == 4N8D == | ||
http://proteopedia.org/wiki/images/a/ac/4n8d_C.png | http://proteopedia.org/wiki/images/a/ac/4n8d_C.png | ||
4N8D with resolution 1.65 Å: an overview of the binding site, missing densities, and clashes. Overall, the missing density sizes are not significant, which gives this crystal a valid structure. And the clashscore is not high, which means it’s not conflicting with the binding site. This crystal seems to be less valid than 6B1E in terms of the RSRZ score, but not enough to be claimed an invalid structure. | 4N8D with resolution 1.65 Å: an overview of the binding site, missing densities, and clashes. Overall, the missing density sizes are not significant, which gives this crystal a valid structure. And the clashscore is not high, which means it’s not conflicting with the binding site. This crystal seems to be less valid than 6B1E in terms of the RSRZ score, but not enough to be claimed an invalid structure. | ||
4N8D: the catalytic triads missing densities are shown. The densities of the amino acids are not significant enough to be viewed as an invalid structure, but does have more missing than the 6B1E crystal. | 4N8D: the catalytic triads missing densities are shown. The densities of the amino acids are not significant enough to be viewed as an invalid structure, but does have more missing than the 6B1E crystal. | ||
http://proteopedia.org/wiki/images/0/06/6b1eeeeejsmol.png | |||
== 4A5S == | == 4A5S == | ||
