MUSCLE v5.3+ supports Multiple Structure Alignment (MStA).
 
Input for structure alignment is a "mega" file generated by the pdb2mega command of Reseek.

# for up to ~100 structures
reseek -pdb2mega STRUCTS -output structs.mega
muscle -align structs.mega -output structs.afa

# for up to ~10,000 structures
reseek -convert STRUCTS -bca structs.bca
reseek -pdb2mega structs.bca -output structs.mega
reseek -distmx structs.bca -output structs.distmx
muscle -super7 structs.mega -distmxin structs.distmx -reseek -output structs.afa