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. Author manuscript; available in PMC: 2011 Dec 16.
Published in final edited form as: J Phys Chem B. 2010 Nov 3;114(49):16290–16297. doi: 10.1021/jp108731r

Figure 1.

Figure 1

Structure of IL-1β (PDB code 6I1B24), with nonpolar residues (cyan) lining the central cavity (green). For a spherical probe of radius 1.4 Å, the volume accessible to the probe center is ∼10 Å3, and the volume covered by the probe sphere (shown in green) is ∼140 Å3. In the most recent crystal structure of IL-1β by Quillin et al.20 (PDB code 2NVH) the volume covered by a probe sphere of 1.4 Å radius is ∼40 Å3. In the other crystal structures,14-17,47 the volume varies between ∼45 and ∼80 Å3. In the amber03/TIP3P MD simulations with occupancy N=0, starting from the NMR structure 6I1B,24 the volume fluctuates about a mean of ∼80 Å3. The larger cavity volume in the NMR structure 6I1B24 is partly a reflection of the fact that it was refined before the use of compactness restraints.48