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.


5fpb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:17, 26 July 2023) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy- 3H,4H-pyrido-3,4-d-pyrimidin-4-one==
==Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy- 3H,4H-pyrido-3,4-d-pyrimidin-4-one==
-
<StructureSection load='5fpb' size='340' side='right' caption='[[5fpb]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
+
<StructureSection load='5fpb' size='340' side='right'caption='[[5fpb]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5fpb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FPB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FPB FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5fpb]] 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=5FPB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FPB FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HA6:2-(1H-PYRAZOL-4-YLOXY)-3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE'>HA6</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]] 1.91&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5fp3|5fp3]], [[5fp4|5fp4]], [[5fp7|5fp7]], [[5fp8|5fp8]], [[5fp9|5fp9]], [[5fpa|5fpa]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HA6:2-(1H-PYRAZOL-4-YLOXY)-3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE'>HA6</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=5fpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fpb OCA], [http://pdbe.org/5fpb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fpb RCSB], [http://www.ebi.ac.uk/pdbsum/5fpb PDBsum]</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=5fpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fpb OCA], [https://pdbe.org/5fpb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fpb RCSB], [https://www.ebi.ac.uk/pdbsum/5fpb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fpb 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 18: Line 19:
</div>
</div>
<div class="pdbe-citations 5fpb" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 5fpb" 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: Chung, C]]
+
[[Category: Homo sapiens]]
-
[[Category: Inhibitor]]
+
[[Category: Large Structures]]
-
[[Category: Jmjd2d]]
+
[[Category: Chung C]]
-
[[Category: Jumonji]]
+
-
[[Category: Kdm4d]]
+
-
[[Category: Lysine specific histone demethylase]]
+
-
[[Category: Oxidoreductase]]
+

Current revision

Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy- 3H,4H-pyrido-3,4-d-pyrimidin-4-one

PDB ID 5fpb

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/5fpb"
Personal tools