FirstGlance/Evaluating Protein Crosslinks: Difference between revisions
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[[5d12]] has two copies of a kinase domain in its [[asymmetric unit]]. FirstGlance reports a possible thioester crosslink only in chain B. The C-S distance is 1.76 Å, quite reasonable. However, the residues are not modeled as a thiester bond, and Jmol draws many spurious "bonds". The sidechain of Asp348 passes through a gap in the all-features electron density (<span style="color:#00a000;font-weight:bold;">green isomesh</span>, above left). The difference electron density map (above right) reveals insufficient density to account for the position of the Asp sidechain (<span style="color:#b00000;font-weight:bold;">dark red isomesh</span>), while suggesting an alternative position for those sidechain atoms (<span style="color:#0000ff;font-weight:bold;">blue isomesh</span>). In conclusion, this is a clash, not a thioester crosslink bond. | [[5d12]] has two copies of a kinase domain in its [[asymmetric unit]]. FirstGlance reports a possible thioester crosslink only in chain B. The C-S distance is 1.76 Å, quite reasonable. However, the residues are not modeled as a thiester bond, and Jmol draws many spurious "bonds". The sidechain of Asp348 passes through a gap in the all-features electron density (<span style="color:#00a000;font-weight:bold;">green isomesh</span>, above left). The difference electron density map (above right) reveals insufficient density to account for the position of the Asp sidechain (<span style="color:#b00000;font-weight:bold;">dark red isomesh</span>), while suggesting an alternative position for those sidechain atoms (<span style="color:#0000ff;font-weight:bold;">blue isomesh</span>). In conclusion, this is a clash, not a thioester crosslink bond. | ||
After [[PDB REDO]] re-refines and rebuilds 5d12, this clash is absent. | |||
===Lys-Cys NOS=== | ===Lys-Cys NOS=== | ||