Table 1. Distribution of interatomic distances between residues lining the S1 and S2 sites in cathepsin K in MD simulations and in X-ray structures.

All distances are given as mean values (± SD) calculated assuming normal distribution of the values. Where multiple distinct populations were observed, ratios between population sizes are given in parentheses.

	Proximal pair		Distal pair
	65Cα-161O	65Cα-161Cβ	66O-160O
Cathepsin K (X-Ray)	7.5 ± 0.2	9.6 ± 0.3	8.3 ± 0.5
Cathepsin K	6.2 ± 0.6	7.5 ± 1.0	7.1 ± 0.5
			8.0 ± 1.2
			(1: 1.7)
Cathepsin K/Substrate	7.6 ± 0.2	9.5 ± 0.4	7.6 ± 0.4
Cathepsin K/NSC13345	6.2 ± 0.6	7.3 ± 0.7	6.8 ± 0.5
		9.2 ± 0.6	7.8 ± 1.0
		(4: 1)	(1.2: 1)
Cathepsin K/NSC94914	4.0 ± 0.4	4.9 ± 0.5	4.3 ± 0.3
	6.2 ± 0.8	7.1 ± 0.7	7.1 ± 1.5
	7.9 ± 0.6	9.3 ± 0.7	(1: 12)
	(1.5: 2.8: 1)	(1: 1.2: 1.1)
Cathepsin K/C4S(1)	7.3 ± 0.7	6.9 ± 0.9	8.3 ± 0.7
		9.2 ± 0.6
		(1: 5.1)
Cathepsin K/C4S(2)	7.5 ± 0.8	9.0 ± 0.7	8.3 ± 0.7
Cathepsin K/C4S(3)	7.5 ± 0.7	7.8 ± 0.8	9.6 ± 0.9