5i13 - Revision history

OCA at 08:19, 23 August 2023

2023-08-23T08:19:45Z

←Older revision		Revision as of 08:19, 23 August 2023
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	<StructureSection load='5i13' size='340' side='right'caption='[[5i13]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5i13' size='340' side='right'caption='[[5i13]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i13]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~I34a1 I34a1~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5fde 5fde]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I13 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I13 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i13]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Puerto_Rico/8/1934(H1N1)) Influenza A virus (A/Puerto Rico/8/1934(H1N1))]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5fde 5fde]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I13 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4P9:4-{(E)-[2-(4-CHLOROPHENYL)HYDRAZINYLIDENE]METHYL}BENZENE-1,2,3-TRIOL'>4P9</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.151Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zi0\|4zi0]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4P9:4-{(E)-[2-(4-CHLOROPHENYL)HYDRAZINYLIDENE]METHYL}BENZENE-1,2,3-TRIOL'>4P9</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211044 I34A1])~~</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=5i13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i13 OCA], [https://pdbe.org/5i13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i13 RCSB], [https://www.ebi.ac.uk/pdbsum/5i13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i13 ProSAT]</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=5i13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i13 OCA], [~~http~~://pdbe.org/5i13 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i13 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i13 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i13 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PA_I34A1 PA_I34A1]] Implicated in endonuclease cleavage of capped RNA primers. Displays an elongation factor activity in viral RNA synthesis. Dispensable for viral transcription, but not replication.	+	[https://www.uniprot.org/uniprot/PA_I34A1 PA_I34A1] Implicated in endonuclease cleavage of capped RNA primers. Displays an elongation factor activity in viral RNA synthesis. Dispensable for viral transcription, but not replication.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: I34a1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fudo, S]]	+	[[Category: Fudo S]]
-	[[Category: Hoshino, T]]	+	[[Category: Hoshino T]]
-	[[Category: Nukaga, M]]	+	[[Category: Nukaga M]]
-	[[Category: Odagiri, T]]	+	[[Category: Odagiri T]]
-	[[Category: Tashiro, M]]	+	[[Category: Tashiro M]]
-	[[Category: Yamamoto, N]]	+	[[Category: Yamamoto N]]
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 07:16, 19 February 2020

2020-02-19T07:16:49Z

←Older revision		Revision as of 07:16, 19 February 2020
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	==Endonuclease inhibitor 2 bound to influenza strain H1N1 polymerase acidic subunit N-terminal region at pH 7.0==		==Endonuclease inhibitor 2 bound to influenza strain H1N1 polymerase acidic subunit N-terminal region at pH 7.0==
-	<StructureSection load='5i13' size='340' side='right' caption='[[5i13]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5i13' size='340' side='right'caption='[[5i13]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i13]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5fde 5fde]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I13 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i13]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/I34a1 I34a1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5fde 5fde]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I13 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4P9:4-{(E)-[2-(4-CHLOROPHENYL)HYDRAZINYLIDENE]METHYL}BENZENE-1,2,3-TRIOL'>4P9</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4P9:4-{(E)-[2-(4-CHLOROPHENYL)HYDRAZINYLIDENE]METHYL}BENZENE-1,2,3-TRIOL'>4P9</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zi0\|4zi0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zi0\|4zi0]]</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=5i13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i13 OCA], [http://pdbe.org/5i13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i13 RCSB], [http://www.ebi.ac.uk/pdbsum/5i13 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211044 I34A1])</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=5i13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i13 OCA], [http://pdbe.org/5i13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i13 RCSB], [http://www.ebi.ac.uk/pdbsum/5i13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i13 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5i13" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5i13" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: I34a1]]
		+	[[Category: Large Structures]]
	[[Category: Fudo, S]]		[[Category: Fudo, S]]
	[[Category: Hoshino, T]]		[[Category: Hoshino, T]]

OCA at 08:39, 1 June 2016

2016-06-01T08:39:38Z

←Older revision		Revision as of 08:39, 1 June 2016
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PA_I34A1 PA_I34A1]] Implicated in endonuclease cleavage of capped RNA primers. Displays an elongation factor activity in viral RNA synthesis. Dispensable for viral transcription, but not replication.		[[http://www.uniprot.org/uniprot/PA_I34A1 PA_I34A1]] Implicated in endonuclease cleavage of capped RNA primers. Displays an elongation factor activity in viral RNA synthesis. Dispensable for viral transcription, but not replication.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Influenza viruses are global threat to humans, and the development of new antiviral agents are still demanded to prepare for pandemics and to overcome the emerging resistance to the current drugs. Influenza polymerase acidic protein N-terminal domain (PAN) has endonuclease activity and is one of the appropriate targets for novel antiviral agents. First, we performed X-ray cocrystal analysis on the complex structures of PAN with two endonuclease inhibitors. The protein crystallization and the inhibitor soaking were done at pH 5.8. The binding modes of the two inhibitors were different from a common binding mode previously reported for the other influenza virus endonuclease inhibitors. We additionally clarified the complex structures of PAN with the same two endonuclease inhibitors at pH 7.0. In one of the crystal structures, an additional inhibitor molecule, which chelated to the two metal ions in the active site, was observed. On the basis of the crystal structures at pH 7.0, we carried out 100 ns molecular dynamics (MD) simulations for both of the complexes. The analysis of simulation results suggested that the binding mode of each inhibitor to PAN was stable in spite of the partial deviation of the simulation structure from the crystal one. Furthermore, crystal structure analysis and MD simulation were performed for PAN in complex with an inhibitor, which was already reported to have a high compound potency for comparison. The findings on the presence of multiple binding sites at around the PAN substrate-binding pocket will provide a hint for enhancing the binding affinity of inhibitors.
		+
		+	Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit.,Fudo S, Yamamoto N, Nukaga M, Odagiri T, Tashiro M, Hoshino T Biochemistry. 2016 May 10;55(18):2646-60. doi: 10.1021/acs.biochem.5b01087. Epub , 2016 Apr 26. PMID:27088785<ref>PMID:27088785</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5i13" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA: Protected "5i13" [edit=sysop:move=sysop]

2016-02-21T02:37:33Z

Protected "5i13" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:37, 21 February 2016

OCA: New page: ==Endonuclease inhibitor 2 bound to influenza strain H1N1 polymerase acidic subunit N-terminal region at pH 7.0== == Structural highlights ==
<table><tr><td colspan='2'>[[5i13]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5fde 5fde]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I13 OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I13 FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=4P9:4-{(E)-[2-(4-CHLOROPHENYL)HYDRAZINYLIDENE]METHYL}BENZENE-1,2,3-TRIOL'>4P9</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[4zi0|4zi0]]</td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5i13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i13 OCA], [http://pdbe.org/5i13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i13 RCSB], [http://www.ebi.ac.uk/pdbsum/5i13 PDBsum]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/PA_I34A1 PA_I34A1]] Implicated in endonuclease cleavage of capped RNA primers. Displays an elongation factor activity in viral RNA synthesis. Dispensable for viral transcription, but not replication.
TOC
</StructureSection>
[[Category: Fudo, S]]
[[Category: Hoshino, T]]
[[Category: Nukaga, M]]
[[Category: Odagiri, T]]
[[Category: Tashiro, M]]
[[Category: Yamamoto, N]]
[[Category: Hydrolase-hydrolase inhibitor complex]]