6n5c - Revision history

OCA at 06:45, 11 October 2023

2023-10-11T06:45:17Z

←Older revision		Revision as of 06:45, 11 October 2023
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	<StructureSection load='6n5c' size='340' side='right'caption='[[6n5c]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6n5c' size='340' side='right'caption='[[6n5c]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n5c]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N5C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N5C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n5c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N5C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KDJ:(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic+acid'>KDJ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.95Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2, HISPPD1, KIAA0433, VIP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KDJ:(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic+acid'>KDJ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n5c OCA], [~~http~~://pdbe.org/6n5c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n5c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n5c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n5c 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=6n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n5c OCA], [https://pdbe.org/6n5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n5c RCSB], [https://www.ebi.ac.uk/pdbsum/6n5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n5c ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VIP2_HUMAN VIP2_HUMAN]] Bifunctional inositol kinase that acts in concert with the IP6K kinases IP6K1, IP6K2 and IP6K3 to synthesize the diphosphate group-containing inositol pyrophosphates diphosphoinositol pentakisphosphate, PP-InsP5, and bis-diphosphoinositol tetrakisphosphate, (PP)2-InsP4. PP-InsP5 and (PP)2-InsP4, also respectively called InsP7 and InsP8, regulate a variety of cellular processes, including apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, insulin signaling and neutrophil activation. Phosphorylates inositol hexakisphosphate (InsP6) at positions 1 or 3 to produce PP-InsP5 which is in turn phosphorylated by IP6Ks to produce (PP)2-InsP4. Alternatively, phosphorylates at position 1 or 3 PP-InsP5, produced by IP6Ks from InsP6, to produce (PP)2-InsP4.<ref>PMID:17690096</ref> <ref>PMID:17702752</ref>	+	[https://www.uniprot.org/uniprot/VIP2_HUMAN VIP2_HUMAN] Bifunctional inositol kinase that acts in concert with the IP6K kinases IP6K1, IP6K2 and IP6K3 to synthesize the diphosphate group-containing inositol pyrophosphates diphosphoinositol pentakisphosphate, PP-InsP5, and bis-diphosphoinositol tetrakisphosphate, (PP)2-InsP4. PP-InsP5 and (PP)2-InsP4, also respectively called InsP7 and InsP8, regulate a variety of cellular processes, including apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, insulin signaling and neutrophil activation. Phosphorylates inositol hexakisphosphate (InsP6) at positions 1 or 3 to produce PP-InsP5 which is in turn phosphorylated by IP6Ks to produce (PP)2-InsP4. Alternatively, phosphorylates at position 1 or 3 PP-InsP5, produced by IP6Ks from InsP6, to produce (PP)2-InsP4.<ref>PMID:17690096</ref> <ref>PMID:17702752</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Potter, B]]	+	[[Category: Potter B]]
-	[[Category: Riley, A]]	+	[[Category: Riley A]]
-	[[Category: Shears~~, S B~~]]	+	[[Category: Shears SB]]
-	[[Category: Wang, H]]	+	[[Category: Wang H]]
-	~~[[Category: Analog]]~~	+
-	~~[[Category: Diphosphoinositol pentakisphosphate]]~~	+
-	~~[[Category: Inositol]]~~	+
-	~~[[Category: Inositol polyphosphate]]~~	+
-	~~[[Category: Inositol pyrophosphate]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Phosphonodifluoroacetamide]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 11:19, 18 December 2019

2019-12-18T11:19:16Z

←Older revision		Revision as of 11:19, 18 December 2019
Line 3:		Line 3:
	<StructureSection load='6n5c' size='340' side='right'caption='[[6n5c]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6n5c' size='340' side='right'caption='[[6n5c]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n5c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N5C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n5c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N5C FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KDJ:(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic+acid'>KDJ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KDJ:(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic+acid'>KDJ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2, HISPPD1, KIAA0433, VIP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n5c OCA], [http://pdbe.org/6n5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n5c RCSB], [http://www.ebi.ac.uk/pdbsum/6n5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n5c 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=6n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n5c OCA], [http://pdbe.org/6n5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n5c RCSB], [http://www.ebi.ac.uk/pdbsum/6n5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n5c ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Potter, B]]		[[Category: Potter, B]]

OCA at 05:54, 21 August 2019

2019-08-21T05:54:49Z

←Older revision		Revision as of 05:54, 21 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n5c is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 5-PCF2Am-InsP5==
		+	<StructureSection load='6n5c' size='340' side='right'caption='[[6n5c]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6n5c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N5C FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KDJ:(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic+acid'>KDJ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n5c OCA], [http://pdbe.org/6n5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n5c RCSB], [http://www.ebi.ac.uk/pdbsum/6n5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n5c ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VIP2_HUMAN VIP2_HUMAN]] Bifunctional inositol kinase that acts in concert with the IP6K kinases IP6K1, IP6K2 and IP6K3 to synthesize the diphosphate group-containing inositol pyrophosphates diphosphoinositol pentakisphosphate, PP-InsP5, and bis-diphosphoinositol tetrakisphosphate, (PP)2-InsP4. PP-InsP5 and (PP)2-InsP4, also respectively called InsP7 and InsP8, regulate a variety of cellular processes, including apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, insulin signaling and neutrophil activation. Phosphorylates inositol hexakisphosphate (InsP6) at positions 1 or 3 to produce PP-InsP5 which is in turn phosphorylated by IP6Ks to produce (PP)2-InsP4. Alternatively, phosphorylates at position 1 or 3 PP-InsP5, produced by IP6Ks from InsP6, to produce (PP)2-InsP4.<ref>PMID:17690096</ref> <ref>PMID:17702752</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Diphosphoinositol phosphates (PP-InsPs) are an evolutionarily ancient group of signalling molecules that are essential to cellular and organismal homeostasis. As the detailed mechanisms of PP-InsP signalling begin to emerge, synthetic analogues of PP-InsPs containing stabilised mimics of the labile diphosphate group can provide valuable investigational tools. We synthesised 5-PCF2Am-InsP5 (1), a novel fluorinated phosphonate analogue of 5-PP-InsP5, and obtained an X-ray crystal structure of 1 in complex with diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2). 5-PCF2Am-InsP5 binds to the kinase domain of PPIP5K2 in a similar orientation to that of the natural substrate 5-PP-InsP5 and the PCF2Am structure can mimic many aspects of the diphosphate group in 5-PP-InsP5. We propose that 1, the structural and electronic properties of which are in some ways complementary to those of existing phosphonoacetate and methylenebisphosphonate analogues of 5-PP-InsP5, may be a useful addition to the expanding array of chemical tools for the investigation of signalling by PP-InsPs. The PCF2Am group may also deserve attention for wider application as a diphosphate mimic.

-	~~Authors: Wang~~, H., Shears, S.B.~~, Riley, A~~., ~~Potter, B~~.	+	Synthesis of an alpha-phosphono-alpha,alpha-difluoroacetamide analogue of the diphosphoinositol pentakisphosphate 5-InsP7.,Riley AM, Wang H, Shears SB, Potter BVL Medchemcomm. 2019 Jun 7;10(7):1165-1172. doi: 10.1039/c9md00163h. eCollection, 2019 Jul 1. PMID:31391889<ref>PMID:31391889</ref>

-	~~Description: Crystal structure~~ of the ~~catalytic domain~~ of ~~PPIP5K2 in complex with AMPPNP and 5~~-~~PCF2Am~~-~~InsP5~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Shears, S.B]]~~	+	<div class="pdbe-citations 6n5c" style="background-color:#fffaf0;"></div>
-	~~[[Category: Wang, H]]~~	+	== References ==
-	[[Category: ~~Riley, A~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Potter, B]]		[[Category: Potter, B]]
		+	[[Category: Riley, A]]
		+	[[Category: Shears, S B]]
		+	[[Category: Wang, H]]
		+	[[Category: Analog]]
		+	[[Category: Diphosphoinositol pentakisphosphate]]
		+	[[Category: Inositol]]
		+	[[Category: Inositol polyphosphate]]
		+	[[Category: Inositol pyrophosphate]]
		+	[[Category: Kinase]]
		+	[[Category: Phosphonodifluoroacetamide]]
		+	[[Category: Transferase]]

OCA at 10:33, 16 January 2019

2019-01-16T10:33:10Z

←Older revision		Revision as of 10:33, 16 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n5c is ON HOLD	+	The entry 6n5c is ON HOLD until Paper Publication

	Authors: Wang, H., Shears, S.B., Riley, A., Potter, B.		Authors: Wang, H., Shears, S.B., Riley, A., Potter, B.
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	Description: Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 5-PCF2Am-InsP5		Description: Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 5-PCF2Am-InsP5
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Potter, B]]
	[[Category: Shears, S.B]]		[[Category: Shears, S.B]]
	[[Category: Wang, H]]		[[Category: Wang, H]]
	[[Category: Riley, A]]		[[Category: Riley, A]]
		+	[[Category: Potter, B]]

OCA: Protected "6n5c" [edit=sysop:move=sysop]

2018-12-02T19:18:21Z

Protected "6n5c" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:18, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n5c is ON HOLD Authors: Wang, H., Shears, S.B., Riley, A., Potter, B. Description: Crystal structure of the catalytic domain of PPIP5K2 in complex...

2018-12-02T19:18:19Z

New page: '''Unreleased structure''' The entry 6n5c is ON HOLD Authors: Wang, H., Shears, S.B., Riley, A., Potter, B. Description: Crystal structure of the catalytic domain of PPIP5K2 in complex...

New page

'''Unreleased structure'''

The entry 6n5c is ON HOLD

Authors: Wang, H., Shears, S.B., Riley, A., Potter, B.

Description: Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 5-PCF2Am-InsP5
[[Category: Unreleased Structures]]
[[Category: Potter, B]]
[[Category: Shears, S.B]]
[[Category: Wang, H]]
[[Category: Riley, A]]