1y3g is a 1 chain structure with sequence from Bacillus thermoproteolyticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Dialkylsilanediols have been found to be an effective functional group for the design of active-site-directed protease inhibitors, including aspartic (HIV protease) and metallo (ACE and thermolysin) proteases. The use of silanediols is predicated on its resemblance to the hydrated carbonyl transition-state structure of amide hydrolysis. This concept has been tested by replacing the presumed tetrahedral carbon of a thermolysin substrate with a silanediol group, resulting in an inhibitor with an inhibition constant K(i) = 40 nM. The structure of the silanediol bound to the active site of thermolysin was found to have a conformation very similar to that of a corresponding phosphonamidate inhibitor (K(i) = 10 nM). In both cases, a single oxygen is within bonding distance to the active-site zinc ion, mimicking the presumed tetrahedral transition state. There are binding differences that appear to be related to the presence or absence of protons on the oxygens attached to the silicon or phosphorus. This is the first crystal structure of an organosilane bound to the active site of a protease.
Structural analysis of silanediols as transition-state-analogue inhibitors of the benchmark metalloprotease thermolysin.,Juers DH, Kim J, Matthews BW, Sieburth SM Biochemistry. 2005 Dec 20;44(50):16524-8. PMID:16342943[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
↑ Juers DH, Kim J, Matthews BW, Sieburth SM. Structural analysis of silanediols as transition-state-analogue inhibitors of the benchmark metalloprotease thermolysin. Biochemistry. 2005 Dec 20;44(50):16524-8. PMID:16342943 doi:10.1021/bi051346v
