How do I use Iridium classification with the SPRUCE workflow (guided Floe) in Orion®?
When using SPRUCE for the preparation of protein receptors for applications such as docking, a user will encounter situations where more than one design unit (DU) for possible use as receptor is generated by SPRUCE. It is up to the user to decide which one is best suited for a particular purpose. Fortunately, SPRUCE provides help to make this decision easier by reporting the Iridium Categories.
SPRUCE will report the following values for the Iridium Category: highly trustworthy (HT), mildly trustworthy (MT), not trustworthy (NT), and not applicable (NA). Iridium relies on the presence of a bound ligand and the availability of electron density data; consequently, all apo structures as well as structures without available electron density data are assigned NA.
While it is preferable to use structures in the HT category, there are cases where none will be available, and the user must choose from MT and, in rare instances, NT structures, although that is not recommended. Spruce will not make decisions for the user, but in addition to the Iridium categories, it provides a simple depiction of Iridium criteria, such as electron density for the ligand and the active site, alternate locations and packing residues, just to name a few. The complete list of Iridium criteria can be found in the documentation.
For HT structures, all the Iridium criteria are fulfilled, and are shown in green (no example shown). For MT structures, some of the criteria are depicted in orange, meaning there could be potential issues, and that they require visual inspection by the user. As an example, the structure of Acetylcholinesterase (PDB accession code 6WV1) is shown in the figure below. Spruce determined that the electron density of the ligand and the active site residues is not sufficient for categorization as HT, as indicated by the orange color. In the 3D viewer, in addition to two atoms in the benzaldehyde oxime ring, electron density is missing for several side chain atoms, such as the Tyr337-OH, Tyr341-OH and Asp74-OD2. Closer inspection reveals that the positions of the active site side chains and ligand atoms are reasonably well defined, making this structure an acceptable choice for docking, in the absence of higher quality alternatives.
The following figure shows a structure of s-adenosylhomocysteine hydrolase (PDB accession code 4PFJ) as an example of Iridium Category NT. The Iridium depiction indicates issues with the ligand and active site electron densities, but in this case, the color red suggests that these issues are critical. A detailed view of the binding site reveals that indeed electron density is missing for several atoms in the ribose ring of the adenosine ligand. In addition, there are multiple side chains with missing electron density, e.g. Asp131, Glu156, Val357 and Ser361. These side chains are close to the bound ligand, but it is not possible to model their precise orientation due to the missing electron density, making this structure unsuitable for use in docking.