4hqx - Revision history

OCA at 15:10, 20 September 2023

OCA — Wed, 20 Sep 2023 15:10:01 GMT

←Older revision		Revision as of 15:10, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4hqx]] is a 2 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=4HQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HQX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4hqx]] is a 2 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=4HQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HQX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=18M:2-O-METHYLGUANOSINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>18M</scene>, <scene name='pdbligand=18Q:2-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>18Q</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=DUZ:5-(BENZYLCARBAMOYL)-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>DUZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE6:PHOSPHORYL-HEXAETHYLENE+GLYCOL'>PE6</scene>, <scene name='pdbligand=UBI:2-DEOXY-5-[(2-METHYLPROPYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UBI</scene>, <scene name='pdbligand=UPE:2-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UPE</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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=18M:2-O-METHYLGUANOSINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>18M</scene>, <scene name='pdbligand=18Q:2-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>18Q</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=DUZ:5-(BENZYLCARBAMOYL)-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>DUZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE6:PHOSPHORYL-HEXAETHYLENE+GLYCOL'>PE6</scene>, <scene name='pdbligand=UBI:2-DEOXY-5-[(2-METHYLPROPYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UBI</scene>, <scene name='pdbligand=UPE:2-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UPE</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=4hqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqx OCA], [https://pdbe.org/4hqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hqx RCSB], [https://www.ebi.ac.uk/pdbsum/4hqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqx 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=4hqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqx OCA], [https://pdbe.org/4hqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hqx RCSB], [https://www.ebi.ac.uk/pdbsum/4hqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqx ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:05, 9 November 2022

OCA — Wed, 09 Nov 2022 08:05:33 GMT

←Older revision		Revision as of 08:05, 9 November 2022
Line 3:		Line 3:
	<StructureSection load='4hqx' size='340' side='right'caption='[[4hqx]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4hqx' size='340' side='right'caption='[[4hqx]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4hqx]] is a 2 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=4HQX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4HQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4hqx]] is a 2 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=4HQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HQX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=18M:2-O-METHYLGUANOSINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>18M</scene>, <scene name='pdbligand=18Q:2-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>18Q</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=DUZ:5-(BENZYLCARBAMOYL)-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>DUZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE6:PHOSPHORYL-HEXAETHYLENE+GLYCOL'>PE6</scene>, <scene name='pdbligand=UBI:2-DEOXY-5-[(2-METHYLPROPYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UBI</scene>, <scene name='pdbligand=UPE:2-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UPE</scene></td></tr>
-	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=18M:2-O-METHYLGUANOSINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>18M</scene>, <scene name='pdbligand=18Q:2-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>18Q</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=DUZ:5-(BENZYLCARBAMOYL)-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>DUZ</scene>, <scene name='pdbligand=PE6:PHOSPHORYL-HEXAETHYLENE+GLYCOL'>PE6</scene>, <scene name='pdbligand=UBI:2-DEOXY-5-[(2-METHYLPROPYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UBI</scene>, <scene name='pdbligand=UPE:2-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UPE</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=4hqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqx OCA], [https://pdbe.org/4hqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hqx RCSB], [https://www.ebi.ac.uk/pdbsum/4hqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqx ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3mjg\|3mjg]], [[4hqu\|4hqu]]~~</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=4hqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqx OCA], [~~http~~://pdbe.org/4hqx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4hqx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4hqx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqx ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.<ref>PMID:12660034</ref>	+	[https://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN] Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.<ref>PMID:12660034</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).	+	[https://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN] Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4hqx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4hqx" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Platelet-derived growth factors and receptors\|Platelet-derived growth factors and receptors]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Davies~~, D R~~]]	+	[[Category: Davies DR]]
-	[[Category: Edwards~~, T E~~]]	+	[[Category: Edwards TE]]
-	[[Category: Gelinas~~, A D~~]]	+	[[Category: Gelinas AD]]
-	[[Category: Janjic, N]]	+	[[Category: Janjic N]]
-	[[Category: Jarvis~~, T C~~]]	+	[[Category: Jarvis TC]]
-	[[Category: Zhang, C]]	+	[[Category: Zhang C]]
-	~~[[Category: 5-modified deoxyuridine]]~~	+
-	~~[[Category: Aptamer]]~~	+
-	~~[[Category: Growth factor]]~~	+
-	~~[[Category: Hormone-dna complex]]~~	+
-	~~[[Category: Selex~~]]	+

OCA at 07:33, 27 March 2019

OCA — Wed, 27 Mar 2019 07:33:27 GMT

←Older revision		Revision as of 07:33, 27 March 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)==		==CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)==
-	<StructureSection load='4hqx' size='340' side='right' caption='[[4hqx]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4hqx' size='340' side='right'caption='[[4hqx]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4hqx]] is a 2 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=4HQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4hqx]] is a 2 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=4HQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQX FirstGlance]. <br>
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 4hqx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4hqx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Platelet-derived growth factors and receptors\|Platelet-derived growth factors and receptors]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Davies, D R]]		[[Category: Davies, D R]]
	[[Category: Edwards, T E]]		[[Category: Edwards, T E]]

OCA at 14:35, 5 August 2016

OCA — Fri, 05 Aug 2016 14:35:35 GMT

←Older revision		Revision as of 14:35, 5 August 2016
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)==		==CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)==
	<StructureSection load='4hqx' size='340' side='right' caption='[[4hqx]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4hqx' size='340' side='right' caption='[[4hqx]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4hqx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4hqx]] is a 2 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=4HQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=18M:2-O-METHYLGUANOSINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>18M</scene>, <scene name='pdbligand=18Q:2-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>18Q</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=DUZ:5-(BENZYLCARBAMOYL)-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>DUZ</scene>, <scene name='pdbligand=PE6:PHOSPHORYL-HEXAETHYLENE+GLYCOL'>PE6</scene>, <scene name='pdbligand=UBI:2-DEOXY-5-[(2-METHYLPROPYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UBI</scene>, <scene name='pdbligand=UPE:2-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UPE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=18M:2-O-METHYLGUANOSINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>18M</scene>, <scene name='pdbligand=18Q:2-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>18Q</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=DUZ:5-(BENZYLCARBAMOYL)-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>DUZ</scene>, <scene name='pdbligand=PE6:PHOSPHORYL-HEXAETHYLENE+GLYCOL'>PE6</scene>, <scene name='pdbligand=UBI:2-DEOXY-5-[(2-METHYLPROPYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UBI</scene>, <scene name='pdbligand=UPE:2-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UPE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3mjg\|3mjg]], [[4hqu\|4hqu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3mjg\|3mjg]], [[4hqu\|4hqu]]</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=4hqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hqx RCSB], [http://www.ebi.ac.uk/pdbsum/4hqx 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=4hqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqx OCA], [http://pdbe.org/4hqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hqx RCSB], [http://www.ebi.ac.uk/pdbsum/4hqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqx ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 21:
	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 4hqx" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Davies, D R]]		[[Category: Davies, D R]]
	[[Category: Edwards, T E]]		[[Category: Edwards, T E]]

OCA at 12:21, 21 December 2014

OCA — Sun, 21 Dec 2014 12:21:35 GMT

←Older revision		Revision as of 12:21, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4hqx\| PDB=4hqx \| SCENE= }}~~	+	==CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)==
-	===CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)===	+	<StructureSection load='4hqx' size='340' side='right' caption='[[4hqx]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23139410}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4hqx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQX FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[http://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.<ref>PMID:12660034</ref>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=18M:2-O-METHYLGUANOSINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>18M</scene>, <scene name='pdbligand=18Q:2-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>18Q</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=DUZ:5-(BENZYLCARBAMOYL)-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>DUZ</scene>, <scene name='pdbligand=PE6:PHOSPHORYL-HEXAETHYLENE+GLYCOL'>PE6</scene>, <scene name='pdbligand=UBI:2-DEOXY-5-[(2-METHYLPROPYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UBI</scene>, <scene name='pdbligand=UPE:2-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UPE</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3mjg\|3mjg]], [[4hqu\|4hqu]]</td></tr>
-	==Function==	+	<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=4hqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hqx RCSB], [http://www.ebi.ac.uk/pdbsum/4hqx PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.<ref>PMID:12660034</ref>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).		[[http://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids. We have exploited synthetic nucleotide modifications that confer protein-like diversity on a nucleic acid scaffold, resulting in a new generation of binding reagents called SOMAmers (Slow Off-rate Modified Aptamers). Here we report a unique crystal structure of a SOMAmer bound to its target, platelet-derived growth factor B (PDGF-BB). The SOMAmer folds into a compact structure and exhibits a hydrophobic binding surface that mimics the interface between PDGF-BB and its receptor, contrasting sharply with mainly polar interactions seen in traditional protein-binding aptamers. The modified nucleotides circumvent the intrinsic diversity constraints of natural nucleic acids, thereby greatly expanding the structural vocabulary of nucleic acid ligands and considerably broadening the range of accessible protein targets.

-	~~==About this Structure==~~	+	Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.,Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter JD, O'Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis TC Proc Natl Acad Sci U S A. 2012 Nov 8. PMID:23139410<ref>PMID:23139410</ref>
-	~~[[4hqx]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4HQX OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Davies, D R.]]	+	[[Category: Davies, D R]]
-	[[Category: Edwards, T E.]]	+	[[Category: Edwards, T E]]
-	[[Category: Gelinas, A D.]]	+	[[Category: Gelinas, A D]]
-	[[Category: Janjic, N.]]	+	[[Category: Janjic, N]]
-	[[Category: Jarvis, T C.]]	+	[[Category: Jarvis, T C]]
-	[[Category: Zhang, C.]]	+	[[Category: Zhang, C]]
	[[Category: 5-modified deoxyuridine]]		[[Category: 5-modified deoxyuridine]]
	[[Category: Aptamer]]		[[Category: Aptamer]]

OCA at 00:03, 25 March 2013

OCA — Mon, 25 Mar 2013 00:03:21 GMT

←Older revision		Revision as of 00:03, 25 March 2013
Line 1:		Line 1:
-	[[Image:4hqx.png\|left\|200px]]
-
	{{STRUCTURE_4hqx\| PDB=4hqx \| SCENE= }}		{{STRUCTURE_4hqx\| PDB=4hqx \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)===		===CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)===
-
	{{ABSTRACT_PUBMED_23139410}}		{{ABSTRACT_PUBMED_23139410}}
		+
		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.<ref>PMID:12660034</ref>
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).

	==About this Structure==		==About this Structure==
	[[4hqx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQX OCA].		[[4hqx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQX OCA].
		+
		+	==Reference==
		+	<references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Davies, D R.]]		[[Category: Davies, D R.]]

OCA at 10:42, 19 December 2012

OCA — Wed, 19 Dec 2012 10:42:53 GMT

←Older revision		Revision as of 10:42, 19 December 2012
Line 1:		Line 1:
-	[[Image:4hqx.~~jpg~~\|left\|200px]]	+	[[Image:4hqx.png\|left\|200px]]

	{{STRUCTURE_4hqx\| PDB=4hqx \| SCENE= }}		{{STRUCTURE_4hqx\| PDB=4hqx \| SCENE= }}

OCA at 09:40, 21 November 2012

OCA — Wed, 21 Nov 2012 09:40:48 GMT

←Older revision		Revision as of 09:40, 21 November 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4hqx.jpg\|left\|200px]]

-	~~The entry~~ 4hqx ~~is ON HOLD~~	+	{{STRUCTURE_4hqx\| PDB=4hqx \| SCENE= }}

-	~~Authors: Davies, D. R., Edwards, T.E., Janjic, N., Gelinas,~~ A~~.D., Zhang, C., Jarvis, T.C.~~	+	===CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)===

-	~~Description~~: ~~CRYSTAL STRUCTURE OF HUMAN PDGF~~-~~BB IN COMPLEX WITH~~ A ~~Modified nucleotide aptamer (SOMAmer SL4)~~	+	{{ABSTRACT_PUBMED_23139410}}
		+
		+	==About this Structure==
		+	[[4hqx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQX OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Davies, D R.]]
		+	[[Category: Edwards, T E.]]
		+	[[Category: Gelinas, A D.]]
		+	[[Category: Janjic, N.]]
		+	[[Category: Jarvis, T C.]]
		+	[[Category: Zhang, C.]]
		+	[[Category: 5-modified deoxyuridine]]
		+	[[Category: Aptamer]]
		+	[[Category: Growth factor]]
		+	[[Category: Hormone-dna complex]]
		+	[[Category: Selex]]

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

OCA — Thu, 08 Nov 2012 13:24:48 GMT

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

←Older revision

Revision as of 13:24, 8 November 2012

OCA: New page: '''Unreleased structure''' The entry 4hqx is ON HOLD Authors: Davies, D. R., Edwards, T.E., Janjic, N., Gelinas, A.D., Zhang, C., Jarvis, T.C. Description: CRYSTAL STRUCTURE OF HUMAN P...

OCA — Thu, 08 Nov 2012 13:24:47 GMT

New page: '''Unreleased structure''' The entry 4hqx is ON HOLD Authors: Davies, D. R., Edwards, T.E., Janjic, N., Gelinas, A.D., Zhang, C., Jarvis, T.C. Description: CRYSTAL STRUCTURE OF HUMAN P...

New page

'''Unreleased structure'''

The entry 4hqx is ON HOLD

Authors: Davies, D. R., Edwards, T.E., Janjic, N., Gelinas, A.D., Zhang, C., Jarvis, T.C.

Description: CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)