Beta-lactamase search in the
pdb database
produces 219 matches. Searching for "tazobactam" results in 5
matches. The entry in the pdb database for this tutorial is
1VM1.
Retrieve the full text pdb entry to your
beta-lactamase tutorial working directory.
- Click on 1VM1
- Click Download/Display File
- Click PDB complete with coordinates TEXT.
- Click"Save full entry to disk".
- If you cannot get the file it is also here1VM1.pdb
This pdb file contains several molecules that were part of the crystal
structure. We will use only the ones that are specifically related to
a molecule of tazobactam bound to the active site of this
beta-lactamase. Much of the information that will help in making the
decisions about what to keep and what to throw away is in the header
of the pdb, so keep the original pdb file around for reference.
The pdb contains:
- One beta-lactamase protein
- One CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE which is the detergent used in crystalizing the complex
- One Tazobactam intermediate TBE in the active site, left after bound tazobactam degraded in the active site during crystalization.
- One Acrylic Acid in active site
- One Tazobactam outside but near the active site
- Some crystal water molecules
We need three parts of the pdb in three separate files at the beginning:
beta-lactamase, TAZ, and TBE.
Make three copies of the pdb file:
vm1_prot.pdb,
vm1_taz.pdb, and vm1_tbe.pdb. Edit each to contain only the molecule that each
is named after.
Make two separate subdirs to treat each of the protein and TAZ setup:
% cp 1VM1.pdb vm1_prot.pdb
% cp 1VM1.pdb vm1_taz.pdb
% cp 1VM1.pdb vm1_tbe.pdb
% mkdir prot_setup
% cp vm1_prot.pdb prot_setup
% mkdir ligand_setup
% cp vm1_taz.pdb ligand_setup
Now set up the molecules for simulation with sander:
Prepare pdb files for the setup utilities.