Path B - Module 22: Structural Auditing (Diagnostics)#

High-resolution structures like 6EQE are excellent, but they are still experimental snapshots. Before you start mutating residues, you must check if the enzyme has any missing atoms or residues that could invalidate your physics calculations.

In this module, you will perform a diagnostic audit of the PETase enzyme.

import molsysmt as msm
from molsysmt import systems

# Load the PETase protein only
petase = msm.convert('pdb:6EQE', to_form='molsysmt.MolSys', selection='molecule_type=="protein"')

1. Identifying Missing Loops#

If the sequence says a residue should be there but the coordinates don’t show it, get_missing_residues() will find it.

missing_res = msm.build.get_missing_residues(petase)
print(f"Missing residues in PETase: {missing_res}")

2. Auditing Heavy Atoms#

Does every residue have its complete sidechain? Broken sidechains can cause errors in potential energy calculations.

missing_atoms = msm.build.get_missing_heavy_atoms(petase)
print(f"Does the enzyme have missing heavy atoms? {len(missing_atoms) > 0}")
if missing_atoms:
    print(f"Broken residues: {missing_atoms}")

3. Natural Connectivity and Cappings#

Is the protein capped? Does it have terminal residues correctly defined? Let’s check for terminal cappings.

cappings = msm.build.get_missing_terminal_cappings(petase)
print(f"Missing terminal cappings: {cappings}")

🏆 Path B Challenge: The Quality Controller#

  1. Load the PDB ID 5XJH (another high-resolution PETase structure).

  2. Use msm.build.has_hydrogens() to see if it was resolved with hydrogens.

  3. Check for Non-Standard Residues in this file using msm.build.get_non_standard_residues().

  4. Audit if there are any missing residues at the C-terminal of the protein.

Your diagnostic is complete. In Module 23, we will use these findings to Repair and Mutate our enzyme to create a thermostable variant.