3t8g

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3t8g]] 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=3T8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T8G FirstGlance]. <br>
<table><tr><td colspan='2'>[[3t8g]] 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=3T8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T8G FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=UBT:N-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-L-LEUCYLGLYCINE'>UBT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3t73|3t73]], [[3t74|3t74]], [[3t87|3t87]], [[3t8c|3t8c]], [[3t8d|3t8d]], [[3t8f|3t8f]], [[3t8h|3t8h]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=UBT:N-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-L-LEUCYLGLYCINE'>UBT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3t8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t8g OCA], [https://pdbe.org/3t8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t8g RCSB], [https://www.ebi.ac.uk/pdbsum/3t8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t8g ProSAT]</span></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=3t8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t8g OCA], [https://pdbe.org/3t8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t8g RCSB], [https://www.ebi.ac.uk/pdbsum/3t8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t8g ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease.
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[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The binding of four congeneric peptide-like thermolysin inhibitors has been studied by high-resolution crystal structure analysis and isothermal titration calorimetry. The ligands differ only by a terminal carboxylate and/or methyl group. A surprising non-additivity of functional group contributions for the carboxylate and/or methyl groups is detected. Adding the methyl first and then the carboxylate group results in a small Gibbs free energy increase and minor enthalpy/entropy partitioning for the first modification, whereas the second involves a strong affinity increase combined with large enthalpy/entropy changes. However, first adding the carboxylate and then the methyl group yields reverse effects: the acidic group attachment now causes minor effects, whereas the added methyl group provokes large changes. As all crystal structures show virtually identical binding modes, affinity changes are related to rearrangements of the first solvation layer next to the S(2)' pocket. About 20-25 water molecules are visible next to the studied complexes. The added COO(-) groups perturb the local water network in both carboxylated complexes, and the attached methyl groups provide favorable interaction sites for water molecules. Apart from one example, a contiguously connected water network between protein and ligand functional groups is observed in all complexes. In the complex with the carboxylated ligand, which still lacks the terminal methyl group, the water network is unfavorably ruptured. This results in a surprising thermodynamic signature showing only a minor affinity increase upon COO(-) group attachment. Because the further added methyl group provides a favorable interaction site for water, the network can be reestablished, and a strong affinity increase with a large enthalpy/entropy signature is then detected.
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Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding.,Biela A, Betz M, Heine A, Klebe G ChemMedChem. 2012 Aug;7(8):1423-34. doi: 10.1002/cmdc.201200206. Epub 2012 Jun, 25. PMID:22733601<ref>PMID:22733601</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3t8g" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Thermolysin 3D structures|Thermolysin 3D structures]]
*[[Thermolysin 3D structures|Thermolysin 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus thermoproteolyticus]]
[[Category: Bacillus thermoproteolyticus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Thermolysin]]
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[[Category: Biela A]]
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[[Category: Biela, A]]
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[[Category: Heine A]]
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[[Category: Heine, A]]
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[[Category: Klebe G]]
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[[Category: Klebe, G]]
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[[Category: Hydrolase-hydrolase inhibitor complex]]
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[[Category: Hydrolysis of peptide bond]]
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[[Category: Metalloprotease]]
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[[Category: Phosphoramidon]]
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[[Category: Protease]]
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Current revision

Thermolysin In Complex With UBTLN26

PDB ID 3t8g

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