2ham - Revision history

OCA at 08:50, 25 October 2023

2023-10-25T08:50:41Z

← Older revision		Revision as of 08:50, 25 October 2023
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	<StructureSection load='2ham' size='340' side='right'caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2ham' size='340' side='right'caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ham]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HAM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HAM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ham]] 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=2HAM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HAM FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=C33:2ALPHA-PROPYL~~-~~1ALPHA~~,~~25-DIHYDROXYVITAMIN+D3'>C33</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]] 1.9Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]~~</~~div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [https://pdbe.org/2ham PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [https://www.ebi.ac.uk/pdbsum/2ham PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ham 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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [https://pdbe.org/2ham PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [https://www.ebi.ac.uk/pdbsum/2ham PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ham ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[https://omim.org/entry/277440 277440]]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>		[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[https://omim.org/entry/277440 277440]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:16252006</ref> <ref>PMID:10678179</ref> <ref>PMID:15728261</ref> <ref>PMID:16913708</ref>		[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:16252006</ref> <ref>PMID:10678179</ref> <ref>PMID:15728261</ref> <ref>PMID:16913708</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hourai, S]]		[[Category: Hourai S]]
	[[Category: Moras, D]]		[[Category: Moras D]]
	[[Category: Rochel, N]]		[[Category: Rochel N]]
	~~[[Category: Alpha-helical sandwich]]~~
	~~[[Category: Gene regulation~~]]

OCA at 10:02, 26 May 2021

2021-05-26T10:02:21Z

← Older revision		Revision as of 10:02, 26 May 2021
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	<StructureSection load='2ham' size='340' side='right'caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2ham' size='340' side='right'caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ham]] 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=2HAM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2HAM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ham]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HAM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HAM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]</div></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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [~~http~~://pdbe.org/2ham PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ham PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ham 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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [https://pdbe.org/2ham PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [https://www.ebi.ac.uk/pdbsum/2ham PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ham ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[~~http~~://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[~~http~~://omim.org/entry/277440 277440]]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>		[[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[https://omim.org/entry/277440 277440]]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:16252006</ref> <ref>PMID:10678179</ref> <ref>PMID:15728261</ref> <ref>PMID:16913708</ref>		[[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:16252006</ref> <ref>PMID:10678179</ref> <ref>PMID:15728261</ref> <ref>PMID:16913708</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Sandbox vdr\|Sandbox vdr]]		*[[Sandbox vdr\|Sandbox vdr]]
	*[[Vitamin D receptor\|Vitamin D receptor]]		*[[Vitamin D receptor 3D structures\|Vitamin D receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:38, 21 August 2019

2019-08-21T07:38:02Z

← Older revision		Revision as of 07:38, 21 August 2019
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	==Crystal structure of VDR LBD complexed to 2alpha-propyl-calcitriol==		==Crystal structure of VDR LBD complexed to 2alpha-propyl-calcitriol==
	<StructureSection load='2ham' size='340' side='right' caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2ham' size='340' side='right'caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ham]] 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=2HAM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HAM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ham]] 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=2HAM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HAM FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ha/2ham_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ha/2ham_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>
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	</div>		</div>
	<div class="pdbe-citations 2ham" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2ham" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Sandbox vdr\|Sandbox vdr]]
			*[[Vitamin D receptor\|Vitamin D receptor]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Hourai, S]]		[[Category: Hourai, S]]
	[[Category: Moras, D]]		[[Category: Moras, D]]

OCA at 00:31, 16 November 2017

2017-11-16T00:31:16Z

← Older revision		Revision as of 00:31, 16 November 2017
Line 1:		Line 1:

	==Crystal structure of VDR LBD complexed to 2alpha-propyl-calcitriol==		==Crystal structure of VDR LBD complexed to 2alpha-propyl-calcitriol==
	<StructureSection load='2ham' size='340' side='right' caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2ham' size='340' side='right' caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]</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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [http://pdbe.org/2ham PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [http://www.ebi.ac.uk/pdbsum/2ham 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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [http://pdbe.org/2ham PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [http://www.ebi.ac.uk/pdbsum/2ham PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ham ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
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	</div>		</div>
	<div class="pdbe-citations 2ham" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2ham" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Sandbox vdr\|Sandbox vdr]]
	*[[Vitamin D receptor\|Vitamin D receptor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:14, 8 February 2016

2016-02-08T17:14:51Z

← Older revision		Revision as of 17:14, 8 February 2016
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	<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=2ham ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:43, 10 September 2015

2015-09-10T13:43:34Z

← Older revision		Revision as of 13:43, 10 September 2015
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	<StructureSection load='2ham' size='340' side='right' caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2ham' size='340' side='right' caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ham]] is a 1 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=2HAM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HAM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ham]] 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=2HAM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HAM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]</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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [http://www.ebi.ac.uk/pdbsum/2ham 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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [http://pdbe.org/2ham PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [http://www.ebi.ac.uk/pdbsum/2ham PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 29:		Line 29:
	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 2ham" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Hourai, S]]		[[Category: Hourai, S]]
	[[Category: Moras, D]]		[[Category: Moras, D]]

OCA at 08:32, 16 January 2015

2015-01-16T08:32:11Z

← Older revision		Revision as of 08:32, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ham]] is a 1 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=2HAM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HAM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ham]] is a 1 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=2HAM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HAM FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]</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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [http://www.ebi.ac.uk/pdbsum/2ham 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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [http://www.ebi.ac.uk/pdbsum/2ham PDBsum]</span></td></tr>
	<table>		</table>
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[http://omim.org/entry/277440 277440]]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>		[[http://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[http://omim.org/entry/277440 277440]]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Hourai, S.]]		[[Category: Hourai, S]]
	[[Category: Moras, D.]]		[[Category: Moras, D]]
	[[Category: Rochel, N.]]		[[Category: Rochel, N]]
	[[Category: Alpha-helical sandwich]]		[[Category: Alpha-helical sandwich]]
	[[Category: Gene regulation]]		[[Category: Gene regulation]]

OCA at 08:11, 30 September 2014

2014-09-30T08:11:29Z

← Older revision		Revision as of 08:11, 30 September 2014
Line 1:		Line 1:
	~~{{STRUCTURE_2ham~~\| ~~PDB~~=2ham \| ~~SCENE~~= }}		==Crystal structure of VDR LBD complexed to 2alpha-propyl-calcitriol==
	===~~Crystal~~ structure of VDR ~~LBD complexed~~ to ~~2alpha~~-propyl-~~calcitriol===~~		<StructureSection load='2ham' size='340' side='right' caption='[[2ham]], [[Resolution\|resolution]] 1.90Å' scene=''>
	~~{{ABSTRACT_PUBMED_16913708}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2ham]] is a 1 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=2HAM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HAM FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C33:2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN+D3'>C33</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1db1\|1db1]], [[1s0z\|1s0z]], [[1s19\|1s19]], [[1ie8\|1ie8]], [[1ie9\|1ie9]], [[1txi\|1txi]], [[2har\|2har]], [[2has\|2has]], [[2hb7\|2hb7]], [[2hb8\|2hb8]]</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=2ham FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ham OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ham RCSB], [http://www.ebi.ac.uk/pdbsum/2ham PDBsum]</span></td></tr>
			<table>
			== Disease ==
			[[http://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[http://omim.org/entry/277440 277440]]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>
			== Function ==
			[[http://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:16252006</ref> <ref>PMID:10678179</ref> <ref>PMID:15728261</ref> <ref>PMID:16913708</ref>
			== 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/ha/2ham_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 ==
			The crystal structure of the vitamin D receptor (VDR) in complex with 1 alpha,25(OH)2D3 revealed the presence of several water molecules near the A-ring linking the ligand C-2 position to the protein surface. Here, we report the crystal structures of the human VDR ligand binding domain bound to selected C-2 alpha substituted analogues, namely, methyl, propyl, propoxy, hydroxypropyl, and hydroxypropoxy. These specific replacements do not modify the structure of the protein or the ligand, but with the exception of the methyl substituent, all analogues affect the presence and/or the location of the above water molecules. The integrity of the channel interactions and specific C-2 alpha analogue directed additional interactions correlate with the binding affinity of the ligands. In contrast, the resulting loss or gain of H-bonds does not reflect the magnitude of HL60 cell differentiation. Our overall findings highlight a rational approach to the design of more potent ligands by building in features revealed in the crystal structures.

	~~==Disease==~~		Probing a water channel near the A-ring of receptor-bound 1 alpha,25-dihydroxyvitamin D3 with selected 2 alpha-substituted analogues.,Hourai S, Fujishima T, Kittaka A, Suhara Y, Takayama H, Rochel N, Moras D J Med Chem. 2006 Aug 24;49(17):5199-205. PMID:16913708<ref>PMID:16913708</ref>
	~~[[http://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Defects in VDR are~~ the ~~cause~~ of ~~rickets vitamin D~~-~~dependent type 2A (VDDR2A) [MIM:[http://omim.org/entry/277440 277440]]~~. A ~~disorder of vitamin~~ D ~~metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism~~. ~~Most patients have total alopecia in addition to rickets~~.~~<ref>PMID:2849209</ref><ref>PMID:8381803</ref><ref>~~PMID:~~1652893</ref><ref>PMID:2177843</ref><ref>PMID:8106618</ref><ref>PMID:8392085</ref><ref>PMID:7828346</ref><ref>PMID:8675579</ref><ref>PMID:8961271</ref>~~<ref>PMID:~~9005998~~</ref>

	~~==Function==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[http:~~/~~/www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Nuclear hormone receptor. Transcription factor that mediates the action~~ of ~~vitamin D3 by controlling~~ the ~~expression of hormone sensitive genes~~. ~~Regulates transcription~~ of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<~~ref~~>~~PMID:16252006</ref><ref>PMID:10678179</ref><ref>PMID:15728261~~</~~ref><ref~~>~~PMID:16913708</ref>~~		</div>

	~~==About this Structure==~~
	[[2ham]] is a 1 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=2HAM OCA].

	==See Also==		==See Also==
			*[[Sandbox vdr\|Sandbox vdr]]
	*[[Vitamin D receptor\|Vitamin D receptor]]		*[[Vitamin D receptor\|Vitamin D receptor]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:016913708</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Hourai, S.]]		[[Category: Hourai, S.]]

OCA at 18:56, 24 March 2013

2013-03-24T18:56:41Z

← Older revision		Revision as of 18:56, 24 March 2013
Line 1:		Line 1:
	~~[[Image:2ham.png\|left\|200px]]~~

	{{STRUCTURE_2ham\| PDB=2ham \| SCENE= }}		{{STRUCTURE_2ham\| PDB=2ham \| SCENE= }}
			===Crystal structure of VDR LBD complexed to 2alpha-propyl-calcitriol===
			{{ABSTRACT_PUBMED_16913708}}

	===~~Crystal structure~~ of ~~VDR LBD complexed~~ to ~~2alpha-propyl-calcitriol===~~		==Disease==
			[[http://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[http://omim.org/entry/277440 277440]]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref><ref>PMID:8381803</ref><ref>PMID:1652893</ref><ref>PMID:2177843</ref><ref>PMID:8106618</ref><ref>PMID:8392085</ref><ref>PMID:7828346</ref><ref>PMID:8675579</ref><ref>PMID:8961271</ref><ref>PMID:9005998</ref>

	~~{{ABSTRACT_PUBMED_16913708}}~~		==Function==
			[[http://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:16252006</ref><ref>PMID:10678179</ref><ref>PMID:15728261</ref><ref>PMID:16913708</ref>

	==About this Structure==		==About this Structure==
Line 14:		Line 16:

	==Reference==		==Reference==
	<ref group="xtra">PMID:016913708</ref><references group="xtra"/>		<ref group="xtra">PMID:016913708</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Hourai, S.]]		[[Category: Hourai, S.]]

OCA: Protected "2ham" [edit=sysop:move=sysop]

2012-10-20T10:52:12Z

Protected "2ham" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:52, 20 October 2012
(No difference)