My approach to this problem would be to use VMD (Visual Molecular Dynamics), where you can load multiple PDBs, perform structural and/or sequence alignment and analyse residue conservation within one program.
VMD is a powerful molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. It is probably an overkill for what you want to do, but I find it rather intuitive to use and powerfull. I also has an amazing documentation and many step-by-step tutorials, starting from this basic introduction.
What you will specifically need for your problem is a MultiSeq 2.0 plugin that you can find under Extensions->Analysis->MultiSeq in new versions of VMD. It is a bioinformatics environment that allows you to load, display, and analyze both sequence and structure data for your proteins within a few mouse clicks. It also has a great set of tutorials to help you start! What you might find interesting for comparing many similar protein structures is an option to create, view and manipulate phylogenetic trees.
Here is step by step tutorial on comparing structures and sequences with MultiSeq.
Here you can find original publications for both VMD and MultiSeq:
Humphrey, W., Dalke, A. and Schulten, K., VMD - Visual Molecular
Dynamics., J. Molec. Graphics, 1996, 14:33-38.
Roberts, E., Eargle, J., Wright, D. and Luthey-Schulten, Z.,
MultiSeq: Unifying sequence and structure data for evolutionary
analysis. BMC Bioinformatics, 2006, 7:382.