View source for 5lif


==Thermolysin in complex with inhibitor==
<StructureSection load='5lif' size='340' side='right'caption='[[5lif]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5lif]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LIF FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.31&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6XO:(2~{S})-3-CYCLOHEXYL-2-[[(2~{S})-4-METHYL-2-[[OXIDANYL(PHENYLMETHOXYCARBONYLAMINOMETHYL)PHOSPHORYL]AMINO]PENTANOYL]AMINO]PROPANOIC+ACID'>6XO</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5lif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lif OCA], [https://pdbe.org/5lif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lif RCSB], [https://www.ebi.ac.uk/pdbsum/5lif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lif ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Kinetic parameters of protein-ligand interactions are progressively acknowledged as valuable information for rational drug discovery. However, a targeted optimization of binding kinetics is not easy to achieve, and further systematic studies are necessary to increase the understanding about molecular mechanisms involved. We determined association and dissociation rate constants for 17 inhibitors of the metalloprotease thermolysin by surface plasmon resonance spectroscopy and correlated kinetic data with high-resolution crystal structures in complex with the protein. From the structure-kinetics relationship, we conclude that the strength of interaction with Asn112 correlates with the rate-limiting step of dissociation. This residue is located at the beginning of a beta-strand motif that lines the binding cleft and is commonly believed to align a substrate for catalysis. A reduced mobility of the Asn112 side chain owing to an enhanced engagement in charge-assisted hydrogen bonds prevents the conformational adjustment associated with ligand release and transformation of the enzyme to its open state. This hypothesis is supported by kinetic data of ZFPLA, a known pseudopeptidic inhibitor of thermolysin, which blocks the conformational transition of Asn112. Interference with this retrograde induced-fit mechanism results in variation of the residence time of thermolysin inhibitors by a factor of 74000. The high conservation of this structural motif within the M4 and M13 metalloprotease families underpins the importance of this feature and has significant implications for drug discovery.

Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin.,Cramer J, Krimmer SG, Fridh V, Wulsdorf T, Karlsson R, Heine A, Klebe G ACS Chem Biol. 2016 Dec 13. PMID:27959500<ref>PMID:27959500</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5lif" style="background-color:#fffaf0;"></div>

==See Also==
*[[Thermolysin 3D structures|Thermolysin 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus thermoproteolyticus]]
[[Category: Large Structures]]
[[Category: Cramer J]]
[[Category: Heine A]]
[[Category: Klebe G]]
[[Category: Krimmer SG]]