Dear Researchers
I have two proteins crystal structures from RCSBD, one is a monomer with two ligands and the other is a dimer with one ligand in each monomer. Both have the same sequence of residues but in monomer, there are 515 residues and in the dimer, there are 505 residues.
I want to get a combined dimer structure in which I may have all the three ligands in both of monomers and residue number may remain 515 rather than 505.
Anyone, please give me your kind suggestions.
Thanks.
Sadaf
Least-square superimpose two copies of the monomer onto the two chains in the dimer, then delete all components you do not wish to retain in the final model and save the remaining parts as a single pdb, if necessary after altering chain/residue labels to make sure not two items have the same identifier. You can do this interactively in most structure visualization programs, e.g. PyMOL, DeepView or UCSF Chimera.
Annemarie Honegger, I combined the residues that I wanted to retain from monomer (506-515) and ligands and residues (27-505) and ligand from dimer, superimposed monomer on two copies of dimer but I am finding a gap between the residues 505 and 506 as shown in the screenshot.
How should I correct this?
Thanks in advance.
If the distance between residue 505 C and residue 506 N is too long for PyMOL to automatically recognize the bond, you may either force a bond by using the "bond" command https://pymolwiki.org/index.php/Bond, or you may change the phi/psi torsion angles in the adjacent residues to bring the two atoms closer together.
If you do energy minimization (outside Pymol), this should also bring the bond length into an acceptable range.
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