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==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 141)==
==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 141)==
<StructureSection load='5plk' size='340' side='right' caption='[[5plk]], [[Resolution|resolution]] 1.14&Aring;' scene=''>
<StructureSection load='5plk' size='340' side='right'caption='[[5plk]], [[Resolution|resolution]] 1.14&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5plk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PLK FirstGlance]. <br>
<table><tr><td colspan='2'>[[5plk]] 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=5PLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PLK 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]] 1.14&#8491;</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=5plk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5plk OCA], [http://pdbe.org/5plk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5plk RCSB], [http://www.ebi.ac.uk/pdbsum/5plk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5plk ProSAT]</span></td></tr>
<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=5plk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5plk OCA], [https://pdbe.org/5plk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5plk RCSB], [https://www.ebi.ac.uk/pdbsum/5plk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5plk ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[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>
[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>  
 
==See Also==
*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arrowsmith, C H]]
[[Category: Homo sapiens]]
[[Category: Bountra, C]]
[[Category: Large Structures]]
[[Category: Bradley, A R]]
[[Category: Arrowsmith CH]]
[[Category: Brandao-Neto, J]]
[[Category: Bountra C]]
[[Category: Brennan, P E]]
[[Category: Bradley AR]]
[[Category: Burgess-Brown, N]]
[[Category: Brandao-Neto J]]
[[Category: Collins, P]]
[[Category: Brennan PE]]
[[Category: Cox, O]]
[[Category: Burgess-Brown N]]
[[Category: Delft, F von]]
[[Category: Collins P]]
[[Category: Dias, A]]
[[Category: Cox O]]
[[Category: Douangamath, A]]
[[Category: Dias A]]
[[Category: Edwards, A]]
[[Category: Douangamath A]]
[[Category: Fairhead, M]]
[[Category: Edwards A]]
[[Category: Krojer, T]]
[[Category: Fairhead M]]
[[Category: MacLean, E]]
[[Category: Krojer T]]
[[Category: Ng, J]]
[[Category: MacLean E]]
[[Category: Oppermann, U]]
[[Category: Ng J]]
[[Category: Pearce, N M]]
[[Category: Oppermann U]]
[[Category: Renjie, Z]]
[[Category: Pearce NM]]
[[Category: Sethi, R]]
[[Category: Renjie Z]]
[[Category: Szykowska, A]]
[[Category: Sethi R]]
[[Category: Talon, R]]
[[Category: Szykowska A]]
[[Category: Vollmar, M]]
[[Category: Talon R]]
[[Category: Wright, N]]
[[Category: Vollmar M]]
[[Category: Epigenetic]]
[[Category: Wright N]]
[[Category: Jmj domain]]
[[Category: Von Delft F]]
[[Category: Oxidoreductase]]
[[Category: Pandda]]
[[Category: Sgc - diamond i04-1 fragment screening]]

Latest revision as of 16:02, 6 March 2024

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 141)PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 141)

Structural highlights

5plk is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.14Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

See Also

References

  1. ↑ Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell. 2006 May 5;125(3):467-81. Epub 2006 Apr 6. PMID:16603238 doi:10.1016/j.cell.2006.03.028

5plk, resolution 1.14Å

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