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==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 6)==
==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 6)==
<StructureSection load='5pht' size='340' side='right' caption='[[5pht]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
<StructureSection load='5pht' size='340' side='right'caption='[[5pht]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5pht]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PHT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PHT FirstGlance]. <br>
<table><tr><td colspan='2'>[[5pht]] 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=5PHT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PHT 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]] 1.83&#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=5pht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pht OCA], [http://pdbe.org/5pht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pht RCSB], [http://www.ebi.ac.uk/pdbsum/5pht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pht 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=5pht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pht OCA], [https://pdbe.org/5pht PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pht RCSB], [https://www.ebi.ac.uk/pdbsum/5pht PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pht 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 15:55, 6 March 2024

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 6)PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 6)

Structural highlights

5pht 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 1.83Å
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

5pht, resolution 1.83Å

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