3fdc - Revision history

OCA at 06:44, 6 September 2023

OCA — Wed, 06 Sep 2023 06:44:54 GMT

←Older revision		Revision as of 06:44, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3fdc' size='340' side='right'caption='[[3fdc]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='3fdc' size='340' side='right'caption='[[3fdc]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3FDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FDC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</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]] 3.1Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [~~http~~://pdbe.org/3fdc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fdc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdc ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</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=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [https://pdbe.org/3fdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [https://www.ebi.ac.uk/pdbsum/3fdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AVID_CHICK AVID_CHICK]] The biological function of avidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of avidin).	+	[https://www.uniprot.org/uniprot/AVID_CHICK AVID_CHICK] The biological function of avidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of avidin).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 38:
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abajian, C]]	+	[[Category: Abajian C]]
-	[[Category: Barker~~, K D~~]]	+	[[Category: Barker KD]]
-	[[Category: Eckermann~~, A L~~]]	+	[[Category: Eckermann AL]]
-	[[Category: Hartings~~, M R~~]]	+	[[Category: Hartings MR]]
-	[[Category: Meade~~, T J~~]]	+	[[Category: Meade TJ]]
-	[[Category: Rosenzweig~~, A C~~]]	+	[[Category: Rosenzweig AC]]
-	[[Category: Sazinsky~~, M H]]~~	+	[[Category: Sazinsky MH]]
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Biotin]]~~	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Polymorphism]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Secreted~~]]	+

OCA at 10:29, 9 September 2020

OCA — Wed, 09 Sep 2020 10:29:34 GMT

←Older revision		Revision as of 10:29, 9 September 2020
Line 1:		Line 1:

	==Crystal Structure of Avidin==		==Crystal Structure of Avidin==
-	<StructureSection load='3fdc' size='340' side='right' caption='[[3fdc]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='3fdc' size='340' side='right'caption='[[3fdc]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3FDC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</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=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [http://pdbe.org/3fdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [http://www.ebi.ac.uk/pdbsum/3fdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdc ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [http://pdbe.org/3fdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [http://www.ebi.ac.uk/pdbsum/3fdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Avidin\|Avidin]]	+	*[[Avidin 3D structures\|Avidin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
		+	[[Category: Large Structures]]
	[[Category: Abajian, C]]		[[Category: Abajian, C]]
	[[Category: Barker, K D]]		[[Category: Barker, K D]]

OCA at 07:49, 5 December 2018

OCA — Wed, 05 Dec 2018 07:49:24 GMT

←Older revision		Revision as of 07:49, 5 December 2018
Line 3:		Line 3:
	<StructureSection load='3fdc' size='340' side='right' caption='[[3fdc]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='3fdc' size='340' side='right' caption='[[3fdc]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Chick Chick~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</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=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [http://pdbe.org/3fdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [http://www.ebi.ac.uk/pdbsum/3fdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdc 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=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [http://pdbe.org/3fdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [http://www.ebi.ac.uk/pdbsum/3fdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdc ProSAT]</span></td></tr>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/3fdc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/3fdc_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chick~~]]	+	[[Category: Gallus gallus]]
	[[Category: Abajian, C]]		[[Category: Abajian, C]]
	[[Category: Barker, K D]]		[[Category: Barker, K D]]
Line 46:		Line 46:
	[[Category: Biotin]]		[[Category: Biotin]]
	[[Category: Glycoprotein]]		[[Category: Glycoprotein]]
		+	[[Category: Polymorphism]]
	[[Category: Protein binding]]		[[Category: Protein binding]]
	[[Category: Secreted]]		[[Category: Secreted]]

OCA at 13:44, 5 August 2016

OCA — Fri, 05 Aug 2016 13:44:20 GMT

←Older revision		Revision as of 13:44, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Avidin==		==Crystal Structure of Avidin==
	<StructureSection load='3fdc' size='340' side='right' caption='[[3fdc]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='3fdc' size='340' side='right' caption='[[3fdc]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Gallus_gallus Gallus gallus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</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=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [http://www.ebi.ac.uk/pdbsum/3fdc 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=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [http://pdbe.org/3fdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [http://www.ebi.ac.uk/pdbsum/3fdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3fdc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	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 3fdc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Gallus gallus~~]]	+	[[Category: Chick]]
	[[Category: Abajian, C]]		[[Category: Abajian, C]]
	[[Category: Barker, K D]]		[[Category: Barker, K D]]

OCA at 19:17, 25 December 2014

OCA — Thu, 25 Dec 2014 19:17:45 GMT

←Older revision		Revision as of 19:17, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [http://www.ebi.ac.uk/pdbsum/3fdc 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=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [http://www.ebi.ac.uk/pdbsum/3fdc PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AVID_CHICK AVID_CHICK]] The biological function of avidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of avidin).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
-	[[Category: Abajian, C.]]	+	[[Category: Abajian, C]]
-	[[Category: Barker, K D.]]	+	[[Category: Barker, K D]]
-	[[Category: Eckermann, A L.]]	+	[[Category: Eckermann, A L]]
-	[[Category: Hartings, M R.]]	+	[[Category: Hartings, M R]]
-	[[Category: Meade, T J.]]	+	[[Category: Meade, T J]]
-	[[Category: Rosenzweig, A C.]]	+	[[Category: Rosenzweig, A C]]
-	[[Category: Sazinsky, M H.]]	+	[[Category: Sazinsky, M H]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Biotin]]		[[Category: Biotin]]

OCA at 11:10, 29 September 2014

OCA — Mon, 29 Sep 2014 11:10:48 GMT

←Older revision		Revision as of 11:10, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:3fdc.~~png\|left~~\|200px]]	+	==Crystal Structure of Avidin==
		+	<StructureSection load='3fdc' size='340' side='right' caption='[[3fdc]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTF:IRON(II)+TETRACYANO-5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-METHYL-[2,2]BIPYRIDINYL-4-YLMETHYL)-AMIDE'>BTF</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fdc RCSB], [http://www.ebi.ac.uk/pdbsum/3fdc PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/3fdc_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Metalloenzymes and electron transfer proteins influence the electrochemical properties of metal cofactors by controlling the second-sphere environment of the protein active site. Properties that tune this environment include the dielectric constant, templated charge structure, van der Waals interactions, and hydrogen bonds. By systematically varying the binding of a redox-active ligand with a protein, we can evaluate how these noncovalent interactions alter the electronic structure of the bound metal complex. For this study, we employ the well-characterized avidin-biotin conjugate as the protein-ligand system, and have synthesized solvatochromic biotinylated and desthiobiotinylated iron(II) bipyridine tetracyano complexes ([Fe(BMB)(CN)(4)](2-) (1) and [Fe(DMB)(CN)(4)](2-) (2)). The binding affinities of 1 and 2 with avidin are 3.5 x 10(7) M(-1) and 1.5 x 10(6) M(-1), respectively. The redox potentials of 1 and 2 (333 mV and 330 mV) shift to 193 mV and 203 mV vs Ag/AgCl when the complex is bound to avidin and adsorbed to a monolayer-coated gold electrode. Upon binding to avidin, the MLCT1 band red-shifts 20 nm for 1 and 10 nm for 2. Similarly, the MLCT2 band for 1 red-shifts 7 nm and the band for 2 red-shifts 6 nm. For comparison, the electronic properties of 1 and 2 were investigated in organic solvents, and similar shifts in the MLCT bands and redox potentials were observed. An X-ray crystal structure of 1 bound to avidin was obtained, and molecular dynamics simulations were performed to analyze the protein environment of the protein-bound transition metal complexes. Our studies demonstrate that changes in the binding affinity of a ligand-receptor pair influence the outer-sphere coordination of the ligand, which in turn affects the electronic properties of the bound complex.

-	~~{{STRUCTURE_3fdc\| PDB=3fdc \| SCENE= }}~~	+	Protein Binding and the Electronic Properties of Iron(II) Complexes: An Electrochemical and Optical Investigation of Outer Sphere Effects.,Barker KD, Eckermann AL, Sazinsky MH, Hartings MR, Abajian C, Georganopoulou D, Ratner MA, Rosenzweig AC, Meade TJ Bioconjug Chem. 2009 Sep 29. PMID:19788194<ref>PMID:19788194</ref>

-	~~===Crystal Structure~~ of ~~Avidin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19788194}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3fdc]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Gallus_gallus Gallus gallus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA].~~	+

	==See Also==		==See Also==
	*[[Avidin\|Avidin]]		*[[Avidin\|Avidin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019788194<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Abajian, C.]]		[[Category: Abajian, C.]]

OCA at 20:27, 20 October 2012

OCA — Sat, 20 Oct 2012 20:27:41 GMT

←Older revision		Revision as of 20:27, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[3fdc]] is a 2 chain structure ~~of [[Avidin]]~~ with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA].	+	[[3fdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA].

	==See Also==		==See Also==

OCA at 10:33, 27 July 2012

OCA — Fri, 27 Jul 2012 10:33:22 GMT

←Older revision		Revision as of 10:33, 27 July 2012
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	[[Image:3fdc.png\|left\|200px]]		[[Image:3fdc.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3fdc", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3fdc\| PDB=3fdc \| SCENE= }}		{{STRUCTURE_3fdc\| PDB=3fdc \| SCENE= }}

	===Crystal Structure of Avidin===		===Crystal Structure of Avidin===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19788194}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19788194 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19788194}}		{{ABSTRACT_PUBMED_19788194}}

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	==See Also==		==See Also==
-	*[[Avidin]]	+	*[[Avidin\|Avidin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19788194~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019788194</ref><references group="xtra"/>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Abajian, C.]]		[[Category: Abajian, C.]]
Line 37:		Line 26:
	[[Category: Biotin]]		[[Category: Biotin]]
	[[Category: Glycoprotein]]		[[Category: Glycoprotein]]
-	[[Category: Polymorphism]]
	[[Category: Protein binding]]		[[Category: Protein binding]]
	[[Category: Secreted]]		[[Category: Secreted]]

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

OCA — Sun, 26 Dec 2010 09:01:17 GMT

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

←Older revision

Revision as of 09:01, 26 December 2010

OCA at 09:01, 26 December 2010

OCA — Sun, 26 Dec 2010 09:01:16 GMT

←Older revision		Revision as of 09:01, 26 December 2010
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-	~~{{Seed}}~~	+	[[Image:3fdc.png\|left\|200px]]
-	[[Image:3fdc.~~jpg~~\|left\|200px]]	+

	<!--		<!--
Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~3FDC~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA].	+	[[3fdc]] is a 2 chain structure of [[Avidin]] with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDC OCA].
		+
		+	==See Also==
		+	*[[Avidin]]

	==Reference==		==Reference==
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	[[Category: Protein binding]]		[[Category: Protein binding]]
	[[Category: Secreted]]		[[Category: Secreted]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 2 10:03:10 2009''