5jt9 - Revision history

OCA at 19:05, 20 September 2023

OCA — Wed, 20 Sep 2023 19:05:36 GMT

←Older revision		Revision as of 19:05, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jt9' size='340' side='right'caption='[[5jt9]], [[Resolution\|resolution]] 1.26Å' scene=''>		<StructureSection load='5jt9' size='340' side='right'caption='[[5jt9]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jt9]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JT9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JT9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jt9]] 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=5JT9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JT9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7AF:~{N}-[(2~{S})-1-[[(2~{S})-2,3-DIMETHYLBUTYL]AMINO]-4-METHYL-1-OXIDANYLIDENE-PENTAN-2-YL]-(PHENYLMETHOXYCARBONYLAMINOMETHYL)PHOSPHONAMIDIC+ACID'>7AF</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>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.26Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7AF:~{N}-[(2~{S})-1-[[(2~{S})-2,3-DIMETHYLBUTYL]AMINO]-4-METHYL-1-OXIDANYLIDENE-PENTAN-2-YL]-(PHENYLMETHOXYCARBONYLAMINOMETHYL)PHOSPHONAMIDIC+ACID'>7AF</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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5jt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt9 OCA], [~~http~~://pdbe.org/5jt9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jt9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jt9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt9 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=5jt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt9 OCA], [https://pdbe.org/5jt9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jt9 RCSB], [https://www.ebi.ac.uk/pdbsum/5jt9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease.	+	[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 ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5jt9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jt9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thermolysin 3D structures\|Thermolysin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	[[Category: Bacillus thermoproteolyticus]]		[[Category: Bacillus thermoproteolyticus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Thermolysin]]~~	+	[[Category: Cramer J]]
-	[[Category: Cramer, J]]	+	[[Category: Heine A]]
-	[[Category: Heine, A]]	+	[[Category: Klebe G]]
-	[[Category: Klebe, G]]	+	[[Category: Krimmer SG]]
-	[[Category: Krimmer~~, S G]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase inhibitor complex]]~~	+
-	~~[[Category: Metalloprotease~~]]	+

OCA at 11:37, 17 June 2020

OCA — Wed, 17 Jun 2020 11:37:21 GMT

←Older revision		Revision as of 11:37, 17 June 2020
Line 1:		Line 1:

	==Thermolysin in complex with JC106.==		==Thermolysin in complex with JC106.==
-	<StructureSection load='5jt9' size='340' side='right' caption='[[5jt9]], [[Resolution\|resolution]] 1.26Å' scene=''>	+	<StructureSection load='5jt9' size='340' side='right'caption='[[5jt9]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jt9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JT9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JT9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jt9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JT9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JT9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7AF:~{N}-[(2~{S})-1-[[(2~{S})-2,3-DIMETHYLBUTYL]AMINO]-4-METHYL-1-OXIDANYLIDENE-PENTAN-2-YL]-(PHENYLMETHOXYCARBONYLAMINOMETHYL)PHOSPHONAMIDIC+ACID'>7AF</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>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7AF:~{N}-[(2~{S})-1-[[(2~{S})-2,3-DIMETHYLBUTYL]AMINO]-4-METHYL-1-OXIDANYLIDENE-PENTAN-2-YL]-(PHENYLMETHOXYCARBONYLAMINOMETHYL)PHOSPHONAMIDIC+ACID'>7AF</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5jt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt9 OCA], [http://pdbe.org/5jt9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jt9 RCSB], [http://www.ebi.ac.uk/pdbsum/5jt9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt9 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt9 OCA], [http://pdbe.org/5jt9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jt9 RCSB], [http://www.ebi.ac.uk/pdbsum/5jt9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus thermoproteolyticus]]		[[Category: Bacillus thermoproteolyticus]]
		+	[[Category: Large Structures]]
	[[Category: Thermolysin]]		[[Category: Thermolysin]]
	[[Category: Cramer, J]]		[[Category: Cramer, J]]

OCA at 21:23, 22 December 2016

OCA — Thu, 22 Dec 2016 21:23:39 GMT

←Older revision		Revision as of 21:23, 22 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jt9 is ~~ON HOLD until Paper~~ Publication	+	==Thermolysin in complex with JC106.==
		+	<StructureSection load='5jt9' size='340' side='right' caption='[[5jt9]], [[Resolution\|resolution]] 1.26Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jt9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JT9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JT9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7AF:~{N}-[(2~{S})-1-[[(2~{S})-2,3-DIMETHYLBUTYL]AMINO]-4-METHYL-1-OXIDANYLIDENE-PENTAN-2-YL]-(PHENYLMETHOXYCARBONYLAMINOMETHYL)PHOSPHONAMIDIC+ACID'>7AF</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt9 OCA], [http://pdbe.org/5jt9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jt9 RCSB], [http://www.ebi.ac.uk/pdbsum/5jt9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt9 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A previously studied congeneric series of thermolysin inhibitors addressing the solvent-accessible S2' pocket with different hydrophobic substituents showed modulations of the surface water layers coating the protein-bound inhibitors. Increasing stabilization of water molecules resulted in an enthalpically more favorable binding signature, overall enhancing affinity. Based on this observation, we optimized the series by designing tailored P2' substituents to improve and further stabilize the surface water network. MD simulations were applied to predict the putative water pattern around the bound ligands. Subsequently, the inhibitors were synthesized and characterized by high-resolution crystallography, microcalorimetry, and surface plasmon resonance. One of the designed inhibitors established the most pronounced water network of all inhibitors tested so far, composed of several fused water polygons, and showed 50-fold affinity enhancement with respect to the original methylated parent ligand. Notably, the inhibitor forming the most perfect water network also showed significantly prolonged residence time compared to the other tested inhibitors.

-	~~Authors: Krimmer, S.G~~., ~~Cramer~~, J., ~~Heine~~, A., Klebe, G.	+	Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands.,Krimmer SG, Cramer J, Betz M, Fridh V, Karlsson R, Heine A, Klebe G J Med Chem. 2016 Dec 8;59(23):10530-10548. Epub 2016 Nov 30. PMID:27933956<ref>PMID:27933956</ref>

-	~~Description: Thermolysin in complex with JC106~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Krimmer, S.G~~]]	+	<div class="pdbe-citations 5jt9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus thermoproteolyticus]]
		+	[[Category: Thermolysin]]
	[[Category: Cramer, J]]		[[Category: Cramer, J]]
-	[[Category: Klebe, G]]
	[[Category: Heine, A]]		[[Category: Heine, A]]
		+	[[Category: Klebe, G]]
		+	[[Category: Krimmer, S G]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase inhibitor complex]]
		+	[[Category: Metalloprotease]]

OCA at 14:37, 26 October 2016

OCA — Wed, 26 Oct 2016 14:37:55 GMT

←Older revision		Revision as of 14:37, 26 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jt9 is ON HOLD	+	The entry 5jt9 is ON HOLD until Paper Publication

	Authors: Krimmer, S.G., Cramer, J., Heine, A., Klebe, G.		Authors: Krimmer, S.G., Cramer, J., Heine, A., Klebe, G.

OCA: Protected "5jt9" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 13:48:06 GMT

Protected "5jt9" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:48, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jt9 is ON HOLD Authors: Krimmer, S.G., Cramer, J., Heine, A., Klebe, G. Description: Thermolysin in complex with JC106. [[Category: Unreleased Str...

OCA — Wed, 01 Jun 2016 13:48:04 GMT

New page: '''Unreleased structure''' The entry 5jt9 is ON HOLD Authors: Krimmer, S.G., Cramer, J., Heine, A., Klebe, G. Description: Thermolysin in complex with JC106. [[Category: Unreleased Str...

New page

'''Unreleased structure'''

The entry 5jt9 is ON HOLD

Authors: Krimmer, S.G., Cramer, J., Heine, A., Klebe, G.

Description: Thermolysin in complex with JC106.
[[Category: Unreleased Structures]]
[[Category: Krimmer, S.G]]
[[Category: Cramer, J]]
[[Category: Klebe, G]]
[[Category: Heine, A]]