5fz3

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==Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3,6-Dihydroxybenzonorbornane (N08776b) (ligand modelled based on PANDDA event map)==
==Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3,6-Dihydroxybenzonorbornane (N08776b) (ligand modelled based on PANDDA event map)==
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<StructureSection load='5fz3' size='340' side='right' caption='[[5fz3]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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<StructureSection load='5fz3' size='340' side='right'caption='[[5fz3]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5fz3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FZ3 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5fz3]] 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=5FZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FZ3 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7SI:(1R,4S)-1,2,3,4-TETRAHYDRO-1,4-METHANONAPHTHALENE-5,8-DIOL'>7SI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5fxv|5fxv]], [[5fxw|5fxw]], [[5fxx|5fxx]], [[5fxz|5fxz]], [[5fy0|5fy0]], [[5fy1|5fy1]], [[5fy4|5fy4]], [[5fy5|5fy5]], [[5fy7|5fy7]], [[5fy8|5fy8]], [[5fy9|5fy9]], [[5fyb|5fyb]], [[5fyc|5fyc]], [[5fyh|5fyh]], [[5fyi|5fyi]], [[5fym|5fym]], [[5fys|5fys]], [[5fyt|5fyt]], [[5fyu|5fyu]], [[5fyv|5fyv]], [[5fyy|5fyy]], [[5fyz|5fyz]], [[5fz0|5fz0]], [[5fz1|5fz1]], [[5fz4|5fz4]], [[5fz6|5fz6]], [[5fz7|5fz7]], [[5fz8|5fz8]], [[5fz9|5fz9]], [[5fza|5fza]], [[5fzb|5fzb]], [[5fzc|5fzc]], [[5fzd|5fzd]], [[5fze|5fze]], [[5fzf|5fzf]], [[5fzg|5fzg]], [[5fzh|5fzh]], [[5fzi|5fzi]], [[5fzk|5fzk]], [[5fzl|5fzl]], [[5fzm|5fzm]], [[5fzo|5fzo]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7SI:(1R,4S)-1,2,3,4-TETRAHYDRO-1,4-METHANONAPHTHALENE-5,8-DIOL'>7SI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<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=5fz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fz3 OCA], [http://pdbe.org/5fz3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fz3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fz3 PDBsum]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5fz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fz3 OCA], [https://pdbe.org/5fz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fz3 RCSB], [https://www.ebi.ac.uk/pdbsum/5fz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fz3 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/KDM5B_HUMAN KDM5B_HUMAN]] Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5. In contrast, may act as a tumor suppressor for melanoma.<ref>PMID:12657635</ref> <ref>PMID:16645588</ref> <ref>PMID:17320161</ref> <ref>PMID:17363312</ref>
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[https://www.uniprot.org/uniprot/KDM5B_HUMAN KDM5B_HUMAN] Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5. In contrast, may act as a tumor suppressor for melanoma.<ref>PMID:12657635</ref> <ref>PMID:16645588</ref> <ref>PMID:17320161</ref> <ref>PMID:17363312</ref>
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==See Also==
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*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
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*[[Lysine-specific histone demethylase 3D structures|Lysine-specific histone demethylase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Arrowsmith, C H]]
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[[Category: Homo sapiens]]
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[[Category: Bountra, C]]
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[[Category: Large Structures]]
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[[Category: Brennan, P E]]
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[[Category: Arrowsmith CH]]
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[[Category: Burgess-Brown, N A]]
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[[Category: Bountra C]]
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[[Category: Collins, P]]
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[[Category: Brennan PE]]
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[[Category: Delft, F Von]]
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[[Category: Burgess-Brown NA]]
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[[Category: Edwards, A M]]
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[[Category: Collins P]]
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[[Category: Gileadi, C]]
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[[Category: Edwards AM]]
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[[Category: Johansson, C]]
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[[Category: Gileadi C]]
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[[Category: Krojer, T]]
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[[Category: Johansson C]]
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[[Category: Kupinska, K]]
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[[Category: Krojer T]]
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[[Category: Nowak, R]]
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[[Category: Kupinska K]]
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[[Category: Oppermann, U]]
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[[Category: Nowak R]]
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[[Category: Pearce, N]]
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[[Category: Oppermann U]]
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[[Category: Strain-Damerell, C]]
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[[Category: Pearce N]]
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[[Category: Szykowska, A]]
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[[Category: Strain-Damerell C]]
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[[Category: Talon, R]]
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[[Category: Szykowska A]]
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[[Category: Diamond i04-1]]
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[[Category: Talon R]]
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[[Category: Fragment screening]]
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[[Category: Von Delft F]]
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[[Category: Jarid1b]]
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[[Category: Oxidoreductase]]
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[[Category: Pandda]]
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[[Category: Plu1]]
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[[Category: Sgc]]
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[[Category: Structural genomic]]
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Current revision

Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3,6-Dihydroxybenzonorbornane (N08776b) (ligand modelled based on PANDDA event map)

PDB ID 5fz3

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