Lab Journal - Task 9 (PAH)

structure selection

The information for the resolution, chain and the positions in PAH can be found on the UniProt entry P00439 itself. The R-factor for the proteins, can be found on the PDBsum entries and the pH values on the pdb entries in the method section.

To check if a gap is included in a structure, we first downloaded the pdb file in text format from the pdb website and then used following unix shell-commands:

grep "^ATOM" 1DMW.pdb > 1DMW.txt
cut -c 23-27 1DMW.txt | uniq > 1DMW_res.txt

Then, we have to check, if the residues are consecutive. Therefore, we wrote a Python-script, which can be invoked as followed:

python test.py

SCWRL

Before generating the mutations with SCWRL, we first had to filter the sequence from the pdb file. Therefore, we used the repairPDB script with following command:

/opt/SS12_Practical/scripts/repairPDB 1J8U.pdb -seq > 1J8U_seq.txt

Afterwards, we had to change the upper letters to lower ones, except for the interesting mutations. For this purpose, we generated a python script: up2low.py ... Then, we can generate a mutation with SCWRL for each sequence file like shown below:

/opt/SS12-Practical/scwrl4/Scwrl4 -i 1J8U.pdb -s 1J8U_seq_mut1.txt -o 1J8U_mut1.pdb

foldX

...