Embedded Files
A human muOR homology model was built using Modeller with 4DKL as the template. The input and output files have been placed on the Google Drive. You can run Modeller on Windows (video) and Mac (video) as well as Linux.
Step 1:I needed to clean the 4DKL PDB file because it contains molecules other than mouse muOR. I deleted all molecules except proteins. I needed to locate T4 Lysozyme which was used to create the crystal. The FASTA (amino acid) sequence of 4DKL was aligned with mouse mu opioid receptor sequence from UniProt:
Step 1:I needed to clean the 4DKL PDB file because it contains molecules other than mouse muOR. I deleted all molecules except proteins. I needed to locate T4 Lysozyme which was used to create the crystal. The FASTA (amino acid) sequence of 4DKL was aligned with mouse mu opioid receptor sequence from UniProt:
64 N-terminal amino acids and 46 C-terminal amino acids are missing from the structure.
You can see that Residue 264-269 (MLSGSK) of mouse muOR is replaced with T4 Lysozyme. I deleted the T4 Lysozyme amino acids from the PDB file to create the template file (In.pdb) for homology modeling.
Mouse and Human muOR sequences were aligned with ClustalOmega.
Mouse and Human muOR sequences were aligned with ClustalOmega.
I created the alignment file by copying and pasting the mouse and human muOR sequences. Note a forward slash "/" was placed between residue 263 and 270. Modeller was used with a python script to create 5 homology models and the model with the best DOPE score was chosen for further analysis. The residue numbers in this file are still wrong. They can be corrected with a python script.
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