Dear All,
We are working on Grhl3 gene in our lab. I am trying to dock two Grhl3 protein to DNA double helix.
As shown in the figure that I’m sending as attached (PDB ID: 5MPF) the two Grhl1-DBD chains are arranged nearly symmetrically to opposite faces of the standard B form 12-base-pair DNA and contact each other via the L10 loop by forming hydrogen-bond interactions (Ming et al.)
The PDB of Grhl3 DBD doesn’t exist. I created a model of Grhl3 DBD by using homology modeling and I create 12-base-pair DNA sequence that Grhl3 DBD binds by using 3D-DART.
Can I prepare this docking with the same way that Grhl1 DBD binding to DNA sequence? Is it possible to dock two proteins that are arranged symmetrically to opposite faces of the DNA?
Thanks!
Hi,
I tried to create this model with 2 Grhl3 proteins, one DNA molecule and a TBL file that created according to the active residues on those 2 Grhl3 proteins and the DNA molecule.
Actually haddock run was successfully performed but the docking was not occurred as I expected. 2 Grhl3 protein molecules are located almost exactly I desired but there is no DNA molecule between them in the created model.
What is wrong with my run? Is it about my input files or the server?
Sincerely.
Halil
Did you use the multi-body server since this is a three body docking problem?
Do you have the correct naming of your DNA bases in the PDB file you submit?
See: https://milou.science.uu.nl/services/HADDOCK2.2/library.html
Yes I did use the multi-body server. I corrected DNA bases as 3 letters and numbered them as if they are one strand. My DNA sequence consist of 12 bp and it is numbered from 1 to 24.
Download the tar archive and the models in the begin dir to see if your dna is there
If not something is wrong in your submisssion