Structural similarity between two proteins is generally given as the root mean square deviation (RMSD) of their atomic positions after they have been structurally aligned.

More on RMSD can be found on wikipedia: https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions.

Any structural alignment program gives you the RMSD value for the superimposed structures. Note also that these programs will try to see if they can get a better fit by disregarding a few residues, and will report how many residues were included in the end for the final calculation. When reporting an RMSD value you should always include also the number of residues that were aligned and the total number of residues.

Usually you only include Calpha atoms in the calculation while disregarding side chains, but you can also do a calculation that includes side chains if comparing very similar structures.

An example of a good tool you can use for pairwise structural alignments is Dali: http://ekhidna.biocenter.helsinki.fi/dali_lite/start

Thank  you Esben, it was helpful.

agreed with what @esben said.

Also,

have you tried Pymol? 

RaptorX Structure Alignment also works very fine http://raptorx.uchicago.edu/DeepAlign/submit/