5pkg: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
m Protected "5pkg" [edit=sysop:move=sysop]
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
'''Unreleased structure'''


The entry 5pkg is ON HOLD
==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 101)==
<StructureSection load='5pkg' size='340' side='right'caption='[[5pkg]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5pkg]] 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=5PKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PKG 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]] 1.54&#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=5pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pkg OCA], [https://pdbe.org/5pkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pkg RCSB], [https://www.ebi.ac.uk/pdbsum/5pkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pkg 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 101)
== 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 16:00, 6 March 2024

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 101)PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 101)

Structural highlights

5pkg 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 1.54Å
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

5pkg, resolution 1.54Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=5pkg&oldid=4081455"