This example uses the crystal structure of a protozoan enoyl-ACP reductase tetramer (PDB 1NNU) to demonstrate the Multi-LZerD web server. Below, each of the four chains has been loaded.
Protein Chains explanation
The clustering cutoff has been left at its default value of 10 Å. Increasing this value would cause more models to be discarded during clustering, thus reducing the running time of the model set scoring.
The surface reduction cutoff has been set to its finest setting of 1e-4. Compared to using e.g. 1e-2, this will slightly increase the running time, but we can be confident that the pairwise docking stage has thoroughly explored the space of possible interactions.
Specifying a job title and comments can help you keep track of your LZerD jobs.
In this example, we know that residue 310 of the large subunits should interact with residue 411 of the small subunits. We also know that residue 397 of each small subunit should be interacting. Residue-residue constraints have been filled in below with these residues. These constraints mean that LZerD will only generate models where each member of these residue pairs are within 5 Å of each other.