This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


5phm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
==PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09455a==
==PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09455a==
-
<StructureSection load='5phm' size='340' side='right' caption='[[5phm]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+
<StructureSection load='5phm' size='340' side='right'caption='[[5phm]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5phm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PHM FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5phm]] 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=5PHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PHM 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=IEJ:O-TOLUENESULFONAMIDE'>IEJ</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]] 1.398&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KDM4D, JHDM3D, JMJD2D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=IEJ:O-TOLUENESULFONAMIDE'>IEJ</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5phm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5phm OCA], [http://pdbe.org/5phm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5phm RCSB], [http://www.ebi.ac.uk/pdbsum/5phm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5phm ProSAT]</span></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=5phm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5phm OCA], [https://pdbe.org/5phm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5phm RCSB], [https://www.ebi.ac.uk/pdbsum/5phm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5phm 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>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 19: Line 19:
</div>
</div>
<div class="pdbe-citations 5phm" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 5phm" style="background-color:#fffaf0;"></div>
 +
 +
==See Also==
 +
*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Human]]
+
[[Category: Homo sapiens]]
-
[[Category: Arrowsmith, C H]]
+
[[Category: Large Structures]]
-
[[Category: Bountra, C]]
+
[[Category: Arrowsmith CH]]
-
[[Category: Bradley, A R]]
+
[[Category: Bountra C]]
-
[[Category: Brandao-Neto, J]]
+
[[Category: Bradley AR]]
-
[[Category: Brennan, P E]]
+
[[Category: Brandao-Neto J]]
-
[[Category: Burgess-Brown, N]]
+
[[Category: Brennan PE]]
-
[[Category: Collins, P]]
+
[[Category: Burgess-Brown N]]
-
[[Category: Cox, O]]
+
[[Category: Collins P]]
-
[[Category: Delft, F von]]
+
[[Category: Cox O]]
-
[[Category: Dias, A]]
+
[[Category: Dias A]]
-
[[Category: Douangamath, A]]
+
[[Category: Douangamath A]]
-
[[Category: Edwards, A]]
+
[[Category: Edwards A]]
-
[[Category: Fairhead, M]]
+
[[Category: Fairhead M]]
-
[[Category: Krojer, T]]
+
[[Category: Krojer T]]
-
[[Category: MacLean, E]]
+
[[Category: MacLean E]]
-
[[Category: Ng, J]]
+
[[Category: Ng J]]
-
[[Category: Oppermann, U]]
+
[[Category: Oppermann U]]
-
[[Category: Pearce, N M]]
+
[[Category: Pearce NM]]
-
[[Category: Renjie, Z]]
+
[[Category: Renjie Z]]
-
[[Category: Sethi, R]]
+
[[Category: Sethi R]]
-
[[Category: Szykowska, A]]
+
[[Category: Szykowska A]]
-
[[Category: Talon, R]]
+
[[Category: Talon R]]
-
[[Category: Vollmar, M]]
+
[[Category: Vollmar M]]
-
[[Category: Wright, N]]
+
[[Category: Wright N]]
-
[[Category: Epigenetic]]
+
[[Category: Von Delft F]]
-
[[Category: Jmj domain]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Pandda]]
+
-
[[Category: Sgc - diamond i04-1 fragment screening]]
+

Revision as of 12:55, 17 January 2024

PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09455a

PDB ID 5phm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5phm"
Personal tools