6gob - Revision history

OCA at 11:32, 24 January 2024

OCA — Wed, 24 Jan 2024 11:32:07 GMT

←Older revision		Revision as of 11:32, 24 January 2024
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	==X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain==		==X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain==
-	<StructureSection load='6gob' size='340' side='right' caption='[[6gob]], [[Resolution\|resolution]] 1.96Å' scene=''>	+	<StructureSection load='6gob' size='340' side='right'caption='[[6gob]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6gob]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GOB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6GOB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6gob]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GOB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F6Q:N,N-pyridylbenzimidazole+derivative-Pd+complex'>F6Q</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PD:PALLADIUM+ION'>PD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.96Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F6Q:N,N-pyridylbenzimidazole+derivative-Pd+complex'>F6Q</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PD:PALLADIUM+ION'>PD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6gob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gob OCA], [~~http~~://pdbe.org/6gob PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6gob RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6gob PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6gob 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=6gob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gob OCA], [https://pdbe.org/6gob PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6gob RCSB], [https://www.ebi.ac.uk/pdbsum/6gob PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6gob ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>	+	[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
-	[[Category: ~~Lysozyme~~]]	+	[[Category: Large Structures]]
-	[[Category: Ferraro, G]]	+	[[Category: Ferraro G]]
-	[[Category: Merlino, A]]	+	[[Category: Merlino A]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: N-pyridylbenzimidazole bidentate ligand]]~~	+
-	~~[[Category: Non covalent bond]]~~	+
-	~~[[Category: Palladium-based drug]]~~	+
-	~~[[Category: Protein-metallodrug interaction]]~~	+
-	~~[[Category: Stacking~~]]	+

OCA at 22:14, 9 August 2018

OCA — Thu, 09 Aug 2018 22:14:14 GMT

←Older revision		Revision as of 22:14, 9 August 2018
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	</div>		</div>
	<div class="pdbe-citations 6gob" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6gob" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:23, 25 July 2018

OCA — Wed, 25 Jul 2018 07:23:42 GMT

←Older revision		Revision as of 07:23, 25 July 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6gob is ~~ON HOLD~~	+	==X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain==
		+	<StructureSection load='6gob' size='340' side='right' caption='[[6gob]], [[Resolution\|resolution]] 1.96Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6gob]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GOB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F6Q:N,N-pyridylbenzimidazole+derivative-Pd+complex'>F6Q</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PD:PALLADIUM+ION'>PD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=6gob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gob OCA], [http://pdbe.org/6gob PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gob RCSB], [http://www.ebi.ac.uk/pdbsum/6gob PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gob ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pd(ii) and Pt(ii) compounds bearing N,N-pyridylbenzimidazole derivatives with an alkylated sulfonate or phosphonium side chain are able to bind the model protein lysozyme both covalently and non-covalently as an entire compound or as a product of a hydrolysis reaction. The interactions with the protein and the origin of the different behaviors of these complexes were unknown hitherto. Here, we present four crystal structures of their adducts with lysozyme. Pt- and Pd-containing fragments bind the protein with different stoichiometries close to the side chains of His15, Asp87, Asp101 and Asn77. The compounds bearing a phosphonium side chain degrade during the reaction with lysozyme. Data show the origin of the non-covalent mode of binding of Pd and Pt compounds bearing a sulfonate side chain, which drives the recognition process by forming a series of H-bonds and coulombic interactions with positively charged residue side chains. In a separate experiment, the structure of the adduct that is formed when the Pd(ii) compound containing an alkylated sulfonate group reacts with ribonuclease A was also determined. In this structure, the sulfonate-Pd(ii) complex binds the side chain of His105 on the surface of the protein and the side chain of the catalytically important His119 residue. Altogether, our data provide a structural basis for understanding the behavior of the analyzed Pd(ii)- and Pt(ii)-based cisplatin analogues in their reactions with proteins and show the first structural characterization of an adduct comprising a cisplatin analogue that is non-covalently bound to a protein. The results suggest that functionalization of a ligand system with a sulfonate group can significantly alter the protein-binding activity and thus the overall pharmacological profile of Pd(ii)- and Pt(ii)-based drugs.

-	~~Authors: Merlino~~, A., Ferraro, G.	+	Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography.,Ferraro G, Mansour AM, Merlino A Dalton Trans. 2018 Jul 13. doi: 10.1039/c8dt01663a. PMID:30004541<ref>PMID:30004541</ref>

-	~~Description: X-ray structure~~ of the ~~adduct formed upon reaction~~ of ~~lysozyme with a Pd(II) complex bearing N,N~~-~~pyridylbenzimidazole derivative with an alkylated sulphonate side chain~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6gob" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gallus gallus]]
		+	[[Category: Lysozyme]]
	[[Category: Ferraro, G]]		[[Category: Ferraro, G]]
	[[Category: Merlino, A]]		[[Category: Merlino, A]]
		+	[[Category: Hydrolase]]
		+	[[Category: N-pyridylbenzimidazole bidentate ligand]]
		+	[[Category: Non covalent bond]]
		+	[[Category: Palladium-based drug]]
		+	[[Category: Protein-metallodrug interaction]]
		+	[[Category: Stacking]]

OCA at 05:52, 14 June 2018

OCA — Thu, 14 Jun 2018 05:52:59 GMT

←Older revision		Revision as of 05:52, 14 June 2018
Line 5:		Line 5:
	Authors: Merlino, A., Ferraro, G.		Authors: Merlino, A., Ferraro, G.

-	Description: X-ray structure of the adduct formed upon reaction af lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain	+	Description: X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ferraro, G]]		[[Category: Ferraro, G]]
	[[Category: Merlino, A]]		[[Category: Merlino, A]]

OCA: Protected "6gob" [edit=sysop:move=sysop]

OCA — Wed, 06 Jun 2018 04:34:32 GMT

Protected "6gob" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:34, 6 June 2018

OCA: New page: '''Unreleased structure''' The entry 6gob is ON HOLD Authors: Merlino, A., Ferraro, G. Description: X-ray structure of the adduct formed upon reaction af lysozyme with a Pd(II) complex...

OCA — Wed, 06 Jun 2018 04:34:31 GMT

New page: '''Unreleased structure''' The entry 6gob is ON HOLD Authors: Merlino, A., Ferraro, G. Description: X-ray structure of the adduct formed upon reaction af lysozyme with a Pd(II) complex...

New page

'''Unreleased structure'''

The entry 6gob is ON HOLD

Authors: Merlino, A., Ferraro, G.

Description: X-ray structure of the adduct formed upon reaction af lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain
[[Category: Unreleased Structures]]
[[Category: Ferraro, G]]
[[Category: Merlino, A]]