Table 2 Simulation setup and components
From: An adaptive peptide-binding site in ubiquitin receptor hRpn13 revealed by structural studies
Simulation | Box Dimensions | Total # atoms | # of water molecules | type of molecule (# of molecules) |
|---|---|---|---|---|
Trimer | a = 85.9, b = 85.9, c = 85.9, α = 60.0, β = 60.0, γ = 60.0 | 44450 | 12853 | Water (12853), salt (81), protein (3), peptide (3) |
Trimer Extension 1 | ||||
Trimer Extension 2 | ||||
Trimer Extension 3 | ||||
Pru-A | a = 59.2, b = 59.2, c = 59.2, α = 60.0, β = 60.0, γ = 60.0 | 14643 | 4234 | Water (4234), salt (4), protein (1), peptide (1) |
Pru-A Extension 1 | ||||
Pru-A Extension 2 | ||||
Pru-A Extension 3 | ||||
Pru-B | a = 65.5, b = 65.5, c = 65.5, α = 60.0, β = 60.0, γ = 60.0 | 19704 | 5911 | Water (5911), salt (35), protein (1), peptide (1) |
Pru-B Extension 1 | ||||
Pru-B Extension 2 | ||||
Pru-B Extension 3 |
