3wbn - Revision history

OCA at 13:02, 8 November 2023

2023-11-08T13:02:49Z

←Older revision		Revision as of 13:02, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='3wbn' size='340' side='right'caption='[[3wbn]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='3wbn' size='340' side='right'caption='[[3wbn]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wbn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pyrfu Pyrfu~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3vvq 3vvq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wbn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3vvq 3vvq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WBN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=OLC:(2R)~~-2~~,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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]] 2.45Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3vvn\|3vvn]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])~~</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=3wbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbn OCA], [https://pdbe.org/3wbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wbn RCSB], [https://www.ebi.ac.uk/pdbsum/3wbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wbn 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=3wbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbn OCA], [https://pdbe.org/3wbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wbn RCSB], [https://www.ebi.ac.uk/pdbsum/3wbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wbn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8U2X0_PYRFU Q8U2X0_PYRFU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyrfu~~]]	+	[[Category: Pyrococcus furiosus DSM 3638]]
-	[[Category: Ishitani, R]]	+	[[Category: Ishitani R]]
-	[[Category: Nureki, O]]	+	[[Category: Nureki O]]
-	[[Category: Tanaka, Y]]	+	[[Category: Tanaka Y]]
-	~~[[Category: Mate]]~~	+
-	~~[[Category: Multidrug transporter]]~~	+
-	~~[[Category: Transport protein-inhibitor complex~~]]	+

OCA at 05:30, 3 August 2022

2022-08-03T05:30:39Z

←Older revision		Revision as of 05:30, 3 August 2022
Line 1:		Line 1:

	==Crystal structure of MATE in complex with MaL6==		==Crystal structure of MATE in complex with MaL6==
-	<StructureSection load='3wbn' size='340' side='right' caption='[[3wbn]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='3wbn' size='340' side='right'caption='[[3wbn]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wbn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pyrfu Pyrfu]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3vvq 3vvq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WBN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wbn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3vvq 3vvq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WBN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vvn\|3vvn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vvn\|3vvn]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=3wbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbn OCA], [~~http~~://pdbe.org/3wbn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wbn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wbn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wbn 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=3wbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbn OCA], [https://pdbe.org/3wbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wbn RCSB], [https://www.ebi.ac.uk/pdbsum/3wbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wbn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyrfu]]		[[Category: Pyrfu]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 07:57, 4 August 2016

2016-08-04T07:57:28Z

←Older revision		Revision as of 07:57, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of MATE in complex with MaL6==		==Crystal structure of MATE in complex with MaL6==
	<StructureSection load='3wbn' size='340' side='right' caption='[[3wbn]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='3wbn' size='340' side='right' caption='[[3wbn]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wbn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3vvq 3vvq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wbn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3vvq 3vvq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WBN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vvn\|3vvn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vvn\|3vvn]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 ~~Pyrococcus furiosus DSM 3638~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=3wbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wbn RCSB], [http://www.ebi.ac.uk/pdbsum/3wbn PDBsum]</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=3wbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbn OCA], [http://pdbe.org/3wbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wbn RCSB], [http://www.ebi.ac.uk/pdbsum/3wbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wbn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3wbn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus furiosus dsm 3638~~]]	+	[[Category: Pyrfu]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]
	[[Category: Nureki, O]]		[[Category: Nureki, O]]

OCA at 09:40, 21 December 2014

2014-12-21T09:40:19Z

←Older revision		Revision as of 09:40, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3wbn\| PDB=3wbn \| SCENE= }}~~	+	==Crystal structure of MATE in complex with MaL6==
-	===Crystal structure of MATE in complex with MaL6===	+	<StructureSection load='3wbn' size='340' side='right' caption='[[3wbn]], [[Resolution\|resolution]] 2.45Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23535598}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wbn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3vvq 3vvq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WBN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vvn\|3vvn]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 Pyrococcus furiosus DSM 3638])</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=3wbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wbn RCSB], [http://www.ebi.ac.uk/pdbsum/3wbn PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Multidrug and toxic compound extrusion (MATE) family transporters are conserved in the three primary domains of life (Archaea, Bacteria and Eukarya), and export xenobiotics using an electrochemical gradient of H(+) or Na(+) across the membrane. MATE transporters confer multidrug resistance to bacterial pathogens and cancer cells, thus causing critical reductions in the therapeutic efficacies of antibiotics and anti-cancer drugs, respectively. Therefore, the development of MATE inhibitors has long been awaited in the field of clinical medicine. Here we present the crystal structures of the H(+)-driven MATE transporter from Pyrococcus furiosus in two distinct apo-form conformations, and in complexes with a derivative of the antibacterial drug norfloxacin and three in vitro selected thioether-macrocyclic peptides, at 2.1-3.0 A resolutions. The structures, combined with functional analyses, show that the protonation of Asp 41 on the amino (N)-terminal lobe induces the bending of TM1, which in turn collapses the N-lobe cavity, thereby extruding the substrate drug to the extracellular space. Moreover, the macrocyclic peptides bind the central cleft in distinct manners, which correlate with their inhibitory activities. The strongest inhibitory peptide that occupies the N-lobe cavity may pave the way towards the development of efficient inhibitors against MATE transporters.

-	~~==About this Structure==~~	+	Structural basis for the drug extrusion mechanism by a MATE multidrug transporter.,Tanaka Y, Hipolito CJ, Maturana AD, Ito K, Kuroda T, Higuchi T, Katoh T, Kato HE, Hattori M, Kumazaki K, Tsukazaki T, Ishitani R, Suga H, Nureki O Nature. 2013 Apr 11;496(7444):247-51. doi: 10.1038/nature12014. Epub 2013 Mar 27. PMID:23535598<ref>PMID:23535598</ref>
-	~~[[3wbn]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. This structure supersedes the now removed PDB entry [http~~:~~//oca.weizmann.ac.il/oca~~-~~bin/send-pdb?obs=1&id=3vvq 3vvq]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3WBN OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023535598</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Pyrococcus furiosus dsm 3638]]		[[Category: Pyrococcus furiosus dsm 3638]]
-	[[Category: Ishitani, R.]]	+	[[Category: Ishitani, R]]
-	[[Category: Nureki, O.]]	+	[[Category: Nureki, O]]
-	[[Category: Tanaka, Y.]]	+	[[Category: Tanaka, Y]]
	[[Category: Mate]]		[[Category: Mate]]
	[[Category: Multidrug transporter]]		[[Category: Multidrug transporter]]
	[[Category: Transport protein-inhibitor complex]]		[[Category: Transport protein-inhibitor complex]]

OCA: Protected "3wbn" [edit=sysop:move=sysop]

2013-06-19T13:18:43Z

Protected "3wbn" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:18, 19 June 2013

OCA: New page: {{STRUCTURE_3wbn| PDB=3wbn | SCENE= }} ===Crystal structure of MATE in complex with MaL6=== {{ABSTRACT_PUBMED_23535598}} ==About this Structure== 3wbn is a 2 chain structure with...

2013-06-19T13:18:40Z

New page: {{STRUCTURE_3wbn| PDB=3wbn | SCENE= }} ===Crystal structure of MATE in complex with MaL6=== {{ABSTRACT_PUBMED_23535598}} ==About this Structure== 3wbn is a 2 chain structure with...

New page

{{STRUCTURE_3wbn| PDB=3wbn | SCENE= }}
===Crystal structure of MATE in complex with MaL6===
{{ABSTRACT_PUBMED_23535598}}

==About this Structure==
[[3wbn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3vvq 3vvq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WBN OCA].

==Reference==
<ref group="xtra">PMID:023535598</ref><references group="xtra"/><references/>
[[Category: Pyrococcus furiosus dsm 3638]]
[[Category: Ishitani, R.]]
[[Category: Nureki, O.]]
[[Category: Tanaka, Y.]]
[[Category: Mate]]
[[Category: Multidrug transporter]]
[[Category: Transport protein-inhibitor complex]]