4kxm - Revision history

OCA at 16:06, 20 September 2023

2023-09-20T16:06:45Z

←Older revision		Revision as of 16:06, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kxm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KXM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kxm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6IA:N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>6IA</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]] 2.24Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6IA:N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>6IA</scene></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=4kxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kxm OCA], [https://pdbe.org/4kxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kxm RCSB], [https://www.ebi.ac.uk/pdbsum/4kxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kxm 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=4kxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kxm OCA], [https://pdbe.org/4kxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kxm RCSB], [https://www.ebi.ac.uk/pdbsum/4kxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kxm ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:20, 7 December 2022

2022-12-07T09:20:18Z

←Older revision		Revision as of 09:20, 7 December 2022
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	==Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP==		==Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP==
-	<StructureSection load='4kxm' size='340' side='right' caption='[[4kxm]], [[Resolution\|resolution]] 2.24Å' scene=''>	+	<StructureSection load='4kxm' size='340' side='right'caption='[[4kxm]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kxm]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KXM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kxm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6IA:N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>6IA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6IA:N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>6IA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fyi\|4fyi]], [[4kxl\|4kxl]], [[4kxn\|4kxn]]</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=4kxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kxm OCA], [https://pdbe.org/4kxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kxm RCSB], [https://www.ebi.ac.uk/pdbsum/4kxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kxm ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dnph1, Rcl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])~~</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=4kxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kxm OCA], [~~http~~://pdbe.org/4kxm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kxm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kxm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kxm ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DNPH1_RAT DNPH1_RAT]] Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.<ref>PMID:17234634</ref>	+	[https://www.uniprot.org/uniprot/DNPH1_RAT DNPH1_RAT] Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.<ref>PMID:17234634</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kaminski, P A~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Labesse, G~~]]	+	[[Category: Kaminski PA]]
-	[[Category: ~~Padilla, A~~]]	+	[[Category: Labesse G]]
-	[[Category: ~~Deoxyribonucleoside 5'-monophosphate n-glycosidase]]~~	+	[[Category: Padilla A]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 15:06, 4 August 2016

2016-08-04T15:06:28Z

←Older revision		Revision as of 15:06, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP==		==Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP==
	<StructureSection load='4kxm' size='340' side='right' caption='[[4kxm]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='4kxm' size='340' side='right' caption='[[4kxm]], [[Resolution\|resolution]] 2.24Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fyi\|4fyi]], [[4kxl\|4kxl]], [[4kxn\|4kxn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fyi\|4fyi]], [[4kxl\|4kxl]], [[4kxn\|4kxn]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dnph1, Rcl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dnph1, Rcl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=4kxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kxm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kxm RCSB], [http://www.ebi.ac.uk/pdbsum/4kxm 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=4kxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kxm OCA], [http://pdbe.org/4kxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kxm RCSB], [http://www.ebi.ac.uk/pdbsum/4kxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kxm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4kxm" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:06, 24 December 2014

2014-12-24T16:06:40Z

←Older revision		Revision as of 16:06, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4kxm\| PDB=4kxm \| SCENE= }}~~	+	==Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP==
-	===Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP===	+	<StructureSection load='4kxm' size='340' side='right' caption='[[4kxm]], [[Resolution\|resolution]] 2.24Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24260472}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4kxm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KXM FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6IA:N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>6IA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fyi\|4fyi]], [[4kxl\|4kxl]], [[4kxn\|4kxn]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dnph1, Rcl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=4kxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kxm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kxm RCSB], [http://www.ebi.ac.uk/pdbsum/4kxm PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/DNPH1_RAT DNPH1_RAT]] Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.<ref>PMID:17234634</ref>		[[http://www.uniprot.org/uniprot/DNPH1_RAT DNPH1_RAT]] Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.<ref>PMID:17234634</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The gene dnph1 (or rcl) encodes a hydrolase that cleaves the 2'-deoxyribonucleoside 5'-monophosphate (dNMP) N-glycosidic bond to yield a free nucleobase and 2-deoxyribose 5-phosphate. Recently, the crystal structure of rat DNPH1, a potential target for anti-cancer therapies, suggested that various analogs of AMP may inhibit this enzyme. From this result, we asked whether N (6)-substituted AMPs, and among them, cytotoxic cytokinin riboside 5'-monophosphates, may inhibit DNPH1. Here, we characterized the structural and thermodynamic aspects of the interactions of these various analogs with DNPH1. Our results indicate that DNPH1 is inhibited by cytotoxic cytokinins at concentrations that inhibit cell growth.

-	~~==About this Structure==~~	+	N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1.,Amiable C, Pochet S, Padilla A, Labesse G, Kaminski PA PLoS One. 2013 Nov 19;8(11):e80755. doi: 10.1371/journal.pone.0080755., eCollection 2013. PMID:24260472<ref>PMID:24260472</ref>
-	~~[[4kxm]] is a 4 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4KXM OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024260472</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Kaminski, P A.]]	+	== References ==
-	[[Category: Labesse, G.]]	+	<references/>
-	[[Category: Padilla, A.]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Buffalo rat]]
		+	[[Category: Kaminski, P A]]
		+	[[Category: Labesse, G]]
		+	[[Category: Padilla, A]]
	[[Category: Deoxyribonucleoside 5'-monophosphate n-glycosidase]]		[[Category: Deoxyribonucleoside 5'-monophosphate n-glycosidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 11:02, 5 February 2014

2014-02-05T11:02:52Z

←Older revision		Revision as of 11:02, 5 February 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4kxm\| PDB=4kxm \| SCENE= }}
		+	===Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP===
		+	{{ABSTRACT_PUBMED_24260472}}

-	~~The entry 4kxm is ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/DNPH1_RAT DNPH1_RAT]] Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.<ref>PMID:17234634</ref>

-	~~Authors~~: ~~Padilla, A~~.~~, Labesse, G~~.~~, Kaminski, P~~.A.	+	==About this Structure==
		+	[[4kxm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KXM OCA].

-	~~Description~~: ~~Crystal structure of DNPH1 (RCL) WITH N6~~-~~ISOPENTENYL~~-~~AMP~~	+	==Reference==
		+	<ref group="xtra">PMID:024260472</ref><references group="xtra"/><references/>
		+	[[Category: Kaminski, P A.]]
		+	[[Category: Labesse, G.]]
		+	[[Category: Padilla, A.]]
		+	[[Category: Deoxyribonucleoside 5'-monophosphate n-glycosidase]]
		+	[[Category: Hydrolase]]

OCA at 15:03, 10 July 2013

2013-07-10T15:03:23Z

←Older revision		Revision as of 15:03, 10 July 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4kxm is ON HOLD	+	The entry 4kxm is ON HOLD until Paper Publication

	Authors: Padilla, A., Labesse, G., Kaminski, P.A.		Authors: Padilla, A., Labesse, G., Kaminski, P.A.

	Description: Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP		Description: Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP

OCA: Protected "4kxm" [edit=sysop:move=sysop]

2013-06-19T12:11:40Z

Protected "4kxm" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:11, 19 June 2013

OCA: New page: '''Unreleased structure''' The entry 4kxm is ON HOLD Authors: Padilla, A., Labesse, G., Kaminski, P.A. Description: Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP

2013-06-19T12:11:39Z

New page: '''Unreleased structure''' The entry 4kxm is ON HOLD Authors: Padilla, A., Labesse, G., Kaminski, P.A. Description: Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP

New page

'''Unreleased structure'''

The entry 4kxm is ON HOLD

Authors: Padilla, A., Labesse, G., Kaminski, P.A.

Description: Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP