5pkc
From Proteopedia
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==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 97)== | ==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 97)== | ||
| - | <StructureSection load='5pkc' size='340' side='right' caption='[[5pkc]], [[Resolution|resolution]] 1.29Å' scene=''> | + | <StructureSection load='5pkc' size='340' side='right'caption='[[5pkc]], [[Resolution|resolution]] 1.29Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5pkc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PKC OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[5pkc]] 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=5PKC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PKC FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.29Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <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> |
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5pkc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pkc OCA], [https://pdbe.org/5pkc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pkc RCSB], [https://www.ebi.ac.uk/pdbsum/5pkc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pkc ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [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> |
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| + | ==See Also== | ||
| + | *[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Arrowsmith | + | [[Category: Homo sapiens]] |
| - | [[Category: Bountra | + | [[Category: Large Structures]] |
| - | [[Category: Bradley | + | [[Category: Arrowsmith CH]] |
| - | [[Category: Brandao-Neto | + | [[Category: Bountra C]] |
| - | [[Category: Brennan | + | [[Category: Bradley AR]] |
| - | [[Category: Burgess-Brown | + | [[Category: Brandao-Neto J]] |
| - | [[Category: Collins | + | [[Category: Brennan PE]] |
| - | [[Category: Cox | + | [[Category: Burgess-Brown N]] |
| - | + | [[Category: Collins P]] | |
| - | [[Category: Dias | + | [[Category: Cox O]] |
| - | [[Category: Douangamath | + | [[Category: Dias A]] |
| - | [[Category: Edwards | + | [[Category: Douangamath A]] |
| - | [[Category: Fairhead | + | [[Category: Edwards A]] |
| - | [[Category: Krojer | + | [[Category: Fairhead M]] |
| - | [[Category: MacLean | + | [[Category: Krojer T]] |
| - | [[Category: Ng | + | [[Category: MacLean E]] |
| - | [[Category: Oppermann | + | [[Category: Ng J]] |
| - | [[Category: Pearce | + | [[Category: Oppermann U]] |
| - | [[Category: Renjie | + | [[Category: Pearce NM]] |
| - | [[Category: Sethi | + | [[Category: Renjie Z]] |
| - | [[Category: Szykowska | + | [[Category: Sethi R]] |
| - | [[Category: Talon | + | [[Category: Szykowska A]] |
| - | [[Category: Vollmar | + | [[Category: Talon R]] |
| - | [[Category: Wright | + | [[Category: Vollmar M]] |
| - | [[Category: | + | [[Category: Wright N]] |
| - | + | [[Category: Von Delft F]] | |
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Current revision
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 97)
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Categories: Homo sapiens | Large Structures | Arrowsmith CH | Bountra C | Bradley AR | Brandao-Neto J | Brennan PE | Burgess-Brown N | Collins P | Cox O | Dias A | Douangamath A | Edwards A | Fairhead M | Krojer T | MacLean E | Ng J | Oppermann U | Pearce NM | Renjie Z | Sethi R | Szykowska A | Talon R | Vollmar M | Wright N | Von Delft F
