If a protein is in dimeric form with 2 chains A and B why is there a need to delete 1 chain. Why cant the chain be kept.? Also is there any rule which chain should be kept and which one should be deleted.
In X-ray crystallography, all the protein chains of a structure are kept, regardless of whether they form dimers or any other form of multimer. Where did you see that one of the chains had to be removed?
The only reason I can think of for not providing both chains would be when the dimer is formed by crystallographic symmetry. In this case the pdb file would contain a single chain, as the dimer is created by building its symmetry mate using the space group and cell dimension information from the pdb file. In a similar way, I guess you could reconstruct a dimer, trimer, etc... from a single chain after removing all other chains (of the same type) from a structure if you are provided with the non-crystallographic symmetry matrices needed for that operation. However, this relies on the assumption that all the molecules in a dimer, trimer, etc... are identical and this is not necessarily true. For example, some dimeric enzymes can only occupy one of their two active sites with substrate, which leads to conformational changes between the two molecules in the dimer.
As Antonio wrote, the pdb file as downloaded from the protein database contains one asymmetric unit of the crystal, independent of the biological unit. only one chain is present in the pdb file of a homodimer if the symmetry axis of the dimer coincides with a crystallographic symmetry axis. If you need the dimer, you have a choice to download the biological assembly (in this case, the two copies may be present as two frames with the same chain label), or to generate the dimer by generating the symmetry-related molecules and extracting an appropriate pair that forms the dimer.
It depends - If the ligand binding sites are far from the dimer interface, it should not do so. On the other hand, if the ligand binds in a left along the dimer interface, you need to use the dimer.
Also, look at the biology of the system: Multimeric enzymes and receptors may display allostery, that is, conformational changes caused by one ligand binding to one monomer may cause conformational changes in the other subunits, either facilitating (positive cooperativity) or hinder (negative cooperatively) by the other subunits.
If you use just one monomer, you have also to pay attention to the possibility of false positive hits of a hydrophobic ligand binding to the exposed hydrophobic dimer interface. In the full dimer, these sites would be hidden in the complex.
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