Path B - Module 21: Surgical Extraction & Deletion#

Welcome, Engineer. Your mission is to optimize the PETase enzyme, a biological catalyst capable of breaking down PET plastics. However, natural enzymes are often unstable at the high temperatures required for industrial recycling.

In this module, you will start by preparing your biocatalyst: isolating the enzyme from its crystal environment.

import molsysmt as msm
from molsysmt import systems

1. Loading the PETase#

We will use the PDB ID 6EQE, the high-resolution structure of the Ideonella sakaiensis PETase.

petase = msm.convert('pdb:6EQE', to_form='molsysmt.MolSys')
msm.info(petase)

2. Cleaning the System#

Crystallographic structures often contain “additives” like glycerol or buffer molecules that are not part of the enzyme. We need to remove them using remove().

# Remove everything that is not protein, water, or the enzyme core
clean_petase = msm.remove(petase, selection='molecule_type=="small molecule"')

print(f"Original entities: {msm.get(petase, element='system', n_entities=True)}")
print(f"Clean entities: {msm.get(clean_petase, element='system', n_entities=True)}")

3. Extracting the Active Site Environment#

If you want to focus your engineering on the catalytic region, you can extract() a sphere around the active site (Ser160, Asp206, His237).

# Extract atoms within 1.0 nm of the catalytic Serine
active_site = msm.extract(clean_petase, selection='within 1.0 nm of (group_id==160 and chain_index==0)')

msm.info(active_site)
msm.view(active_site)

🏆 Path B Challenge: The Site Isolator#

  1. Load the PETase (6EQE) again.

  2. Extract only the protein (remove water and everything else).

  3. Use msm.info(element='chain') to verify you have a single clean chain.

  4. Save the result as a variable enzyme_core for the next modules.

You have isolated the engine of your project. In Module 22, we will perform a Structural Audit to ensure this enzyme is physically ready for engineering.