5pmh: Difference between revisions

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New page: '''Unreleased structure''' The entry 5pmh is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of JMJD2D after initial refinement with no li...
 
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'''Unreleased structure'''


The entry 5pmh is ON HOLD
==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 175)==
<StructureSection load='5pmh' size='340' side='right'caption='[[5pmh]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5pmh]] 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=5PMH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PMH FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.52&#8491;</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=5pmh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pmh OCA], [https://pdbe.org/5pmh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pmh RCSB], [https://www.ebi.ac.uk/pdbsum/5pmh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pmh ProSAT]</span></td></tr>
</table>
== 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>


Authors: Krojer, T.
==See Also==
 
*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
Description: PanDDA analysis group deposition --Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 175)
== References ==
[[Category: Unreleased Structures]]
<references/>
[[Category: Krojer, T]]
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Arrowsmith CH]]
[[Category: Bountra C]]
[[Category: Bradley AR]]
[[Category: Brandao-Neto J]]
[[Category: Brennan PE]]
[[Category: Burgess-Brown N]]
[[Category: Collins P]]
[[Category: Cox O]]
[[Category: Dias A]]
[[Category: Douangamath A]]
[[Category: Edwards A]]
[[Category: Fairhead M]]
[[Category: Krojer T]]
[[Category: MacLean E]]
[[Category: Ng J]]
[[Category: Oppermann U]]
[[Category: Pearce NM]]
[[Category: Renjie Z]]
[[Category: Sethi R]]
[[Category: Szykowska A]]
[[Category: Talon R]]
[[Category: Vollmar M]]
[[Category: Wright N]]
[[Category: Von Delft F]]

Latest revision as of 16:04, 6 March 2024

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 175)PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 175)

Structural highlights

5pmh 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 1.52Å
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

5pmh, resolution 1.52Å

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