4hon: Difference between revisions

← Older edit Newer edit →

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

OCA

@@ Line 1: / Line 1: @@
 ==Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate==
-<StructureSection load='4hon' size='340' side='right' caption='[[4hon]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='4hon' size='340' side='right'caption='[[4hon]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4hon]] is a 4 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=4HON OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HON FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4hon]] is a 4 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=4HON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HON FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</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=4hon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hon OCA], [https://pdbe.org/4hon PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hon RCSB], [https://www.ebi.ac.uk/pdbsum/4hon PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hon ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">JHDM3D, JMJD2D, KDM4D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4hon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hon OCA], [http://pdbe.org/4hon PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hon RCSB], [http://www.ebi.ac.uk/pdbsum/4hon PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hon ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 18: @@
 </div>
 <div class="pdbe-citations 4hon" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Krishnan, S]]
+[[Category: Large Structures]]
-[[Category: Trievel, R C]]
+[[Category: Krishnan S]]
-[[Category: Beta barrel fold]]
+[[Category: Trievel RC]]
-[[Category: Jmjd2/kdm4 family]]
-[[Category: Jumonji c demethylase]]
-[[Category: Oxidoreductase]]