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. Author manuscript; available in PMC: 2012 Mar 11.
Published in final edited form as: J Mol Biol. 2010 Dec 9;406(5):713–729. doi: 10.1016/j.jmb.2010.12.005

Figure 8.

Figure 8

The binding pockets from the catalytic domains of two different stromelysin (pocket 29 from PDB 1hv5 chain A and pocket 19 from 1qic chain D). The two pockets align well with an cRMSD of 0.76Å for 29 atoms from 10 different residues. The structurally aligned residues are placed in the order given by primary sequence sequence of 1hv5. A sequence order dependent structural alignment method would not be able to generate this alignment as aligned atoms from both proteins do not follow the order given by their respective primary sequences.