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5pmv

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==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 189)==
==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 189)==
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<StructureSection load='5pmv' size='340' side='right' caption='[[5pmv]], [[Resolution|resolution]] 1.34&Aring;' scene=''>
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<StructureSection load='5pmv' size='340' side='right'caption='[[5pmv]], [[Resolution|resolution]] 1.34&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5pmv]] 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=5PMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PMV FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5pmv]] 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=5PMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PMV FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.34&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KDM4D, JHDM3D, JMJD2D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<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=5pmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pmv OCA], [http://pdbe.org/5pmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pmv RCSB], [http://www.ebi.ac.uk/pdbsum/5pmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pmv ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5pmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pmv OCA], [https://pdbe.org/5pmv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pmv RCSB], [https://www.ebi.ac.uk/pdbsum/5pmv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pmv ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/KDM4D_HUMAN KDM4D_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate.<ref>PMID:16603238</ref>
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[https://www.uniprot.org/uniprot/KDM4D_HUMAN KDM4D_HUMAN] Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate.<ref>PMID:16603238</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
</div>
<div class="pdbe-citations 5pmv" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 5pmv" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Human]]
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[[Category: Homo sapiens]]
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[[Category: Arrowsmith, C H]]
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[[Category: Large Structures]]
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[[Category: Bountra, C]]
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[[Category: Arrowsmith CH]]
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[[Category: Bradley, A R]]
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[[Category: Bountra C]]
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[[Category: Brandao-Neto, J]]
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[[Category: Bradley AR]]
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[[Category: Brennan, P E]]
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[[Category: Brandao-Neto J]]
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[[Category: Burgess-Brown, N]]
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[[Category: Brennan PE]]
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[[Category: Collins, P]]
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[[Category: Burgess-Brown N]]
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[[Category: Cox, O]]
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[[Category: Collins P]]
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[[Category: Delft, F von]]
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[[Category: Cox O]]
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[[Category: Dias, A]]
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[[Category: Dias A]]
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[[Category: Douangamath, A]]
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[[Category: Douangamath A]]
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[[Category: Edwards, A]]
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[[Category: Edwards A]]
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[[Category: Fairhead, M]]
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[[Category: Fairhead M]]
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[[Category: Krojer, T]]
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[[Category: Krojer T]]
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[[Category: MacLean, E]]
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[[Category: MacLean E]]
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[[Category: Ng, J]]
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[[Category: Ng J]]
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[[Category: Oppermann, U]]
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[[Category: Oppermann U]]
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[[Category: Pearce, N M]]
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[[Category: Pearce NM]]
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[[Category: Renjie, Z]]
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[[Category: Renjie Z]]
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[[Category: Sethi, R]]
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[[Category: Sethi R]]
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[[Category: Szykowska, A]]
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[[Category: Szykowska A]]
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[[Category: Talon, R]]
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[[Category: Talon R]]
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[[Category: Vollmar, M]]
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[[Category: Vollmar M]]
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[[Category: Wright, N]]
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[[Category: Wright N]]
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[[Category: Epigenetic]]
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[[Category: Von Delft F]]
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[[Category: Jmj domain]]
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[[Category: Oxidoreductase]]
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[[Category: Pandda]]
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[[Category: Sgc - diamond i04-1 fragment screening]]
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Revision as of 13:03, 17 January 2024

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 189)

PDB ID 5pmv

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