5ma7: Difference between revisions
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<StructureSection load='5ma7' size='340' side='right'caption='[[5ma7]], [[Resolution|resolution]] 1.30Å' scene=''> | <StructureSection load='5ma7' size='340' side='right'caption='[[5ma7]], [[Resolution|resolution]] 1.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ma7]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5ma7]] 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=5MA7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MA7 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7K0:(2~{S})-2-[[(2~{S})-3-azanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]propanoyl]amino]-4-methyl-pentanoic+acid'>7K0</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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7K0:(2~{S})-2-[[(2~{S})-3-azanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]propanoyl]amino]-4-methyl-pentanoic+acid'>7K0</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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ma7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ma7 OCA], [https://pdbe.org/5ma7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ma7 RCSB], [https://www.ebi.ac.uk/pdbsum/5ma7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ma7 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 5ma7" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5ma7" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Thermolysin 3D structures|Thermolysin 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Bacillus thermoproteolyticus]] | [[Category: Bacillus thermoproteolyticus]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Cramer J]] | |||
[[Category: Cramer | [[Category: Heine A]] | ||
[[Category: Heine | [[Category: Klebe G]] | ||
[[Category: Klebe | [[Category: Krimmer SG]] | ||
[[Category: Krimmer | |||
Latest revision as of 21:34, 1 November 2023
Structure of thermolysin in complex with inhibitor (JC306).Structure of thermolysin in complex with inhibitor (JC306).
Structural highlights
FunctionTHER_BACTH Extracellular zinc metalloprotease. Publication Abstract from PubMedWe investigated the hydration state of the deep, well-accessible hydrophobic S1' specificity pocket of the metalloprotease thermolysin with purposefully designed ligands using high-resolution crystallography and isothermal titration calorimetry. The S1' pocket is known to recognize selectively a very stringent set of aliphatic side chains such as valine, leucine, and isoleucine of putative substrates. We engineered a weak-binding ligand covering the active site of the protease without addressing the S1' pocket, thus transforming it into an enclosed cavity. Its sustained accessibility could be proved by accommodating noble gas atoms into the pocket in the crystalline state. The topology and electron content of the enclosed pocket with a volume of 141 A3 were analyzed using an experimental MAD-phased electron density map that was calibrated to an absolute electron number scale, enabling access to the total electron content within the cavity. Our analysis indicates that the S1' pocket is virtually vacated, thus free of any water molecules. The thermodynamic signature of the reduction of the void within the pocket by growing aliphatic P1' substituents (H, Me, iPr, iBu) reveals a dramatic, enthalpy-dominated gain in free energy of binding resulting in a factor of 41000 in Kd for the H-to-iBu transformation. Substituents placing polar decoy groups into the pocket to capture putatively present water molecules could not collect any evidence for a bound solvent molecule. How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin.,Krimmer SG, Cramer J, Schiebel J, Heine A, Klebe G J Am Chem Soc. 2017 Aug 2;139(30):10419-10431. doi: 10.1021/jacs.7b05028. Epub, 2017 Jul 24. PMID:28696673[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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