2vcg

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Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17

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Categories: Alcaligenes sp | Large Structures | Dickmanns A | Ficner R | Strasser A

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-[[Image:2vcg.jpg|left|200px]]
- {{Structure
+==Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17==
-|PDB= 2vcg |SIZE=350|CAPTION= <scene name='initialview01'>2vcg</scene>, resolution 1.90&Aring;
+<StructureSection load='2vcg' size='340' side='right'caption='[[2vcg]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Gol+Binding+Site+For+Chain+D'>AC1</scene>, <scene name='pdbsite=AC2:Gol+Binding+Site+For+Chain+C'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Zn+Binding+Site+For+Chain+B'>AC4</scene>, <scene name='pdbsite=AC5:Zn+Binding+Site+For+Chain+C'>AC5</scene>, <scene name='pdbsite=AC6:Zn+Binding+Site+For+Chain+D'>AC6</scene>, <scene name='pdbsite=AC7:Zn+Binding+Site+For+Chain+D'>AC7</scene>, <scene name='pdbsite=AC8:K+Binding+Site+For+Chain+A'>AC8</scene>, <scene name='pdbsite=AC9:K+Binding+Site+For+Chain+B'>AC9</scene>, <scene name='pdbsite=BC1:K+Binding+Site+For+Chain+C'>BC1</scene>, <scene name='pdbsite=BC2:K+Binding+Site+For+Chain+D'>BC2</scene>, <scene name='pdbsite=BC3:K+Binding+Site+For+Chain+A'>BC3</scene>, <scene name='pdbsite=BC4:K+Binding+Site+For+Chain+B'>BC4</scene>, <scene name='pdbsite=BC5:K+Binding+Site+For+Chain+C'>BC5</scene>, <scene name='pdbsite=BC6:K+Binding+Site+For+Chain+D'>BC6</scene>, <scene name='pdbsite=BC7:S17+Binding+Site+For+Chain+D'>BC7</scene>, <scene name='pdbsite=BC8:S17+Binding+Site+For+Chain+C'>BC8</scene>, <scene name='pdbsite=BC9:S17+Binding+Site+For+Chain+A'>BC9</scene>, <scene name='pdbsite=CC1:S17+Binding+Site+For+Chain+B'>CC1</scene> and <scene name='pdbsite=CC2:Cl+Binding+Site+For+Chain+D'>CC2</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=S17:METHYL+4-BROMO-N-[8-(HYDROXYAMINO)-8-OXOOCTANOYL]-L-PHENYLALANINATE'>S17</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[2vcg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_sp. Alcaligenes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VCG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VCG FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=S17:METHYL+4-BROMO-N-[8-(HYDROXYAMINO)-8-OXOOCTANOYL]-L-PHENYLALANINATE'>S17</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vcg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vcg OCA], [https://pdbe.org/2vcg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vcg RCSB], [https://www.ebi.ac.uk/pdbsum/2vcg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vcg ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1zz1|1ZZ1]], [[1zz0|1ZZ0]], [[1zz3|1ZZ3]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vcg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vcg OCA], [http://www.ebi.ac.uk/pdbsum/2vcg PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2vcg RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/HDAH_ALCSD HDAH_ALCSD]
+== Evolutionary Conservation ==
-'''CRYSTAL STRUCTURE OF A HDAC-LIKE PROTEIN HDAH FROM BORDETELLA SP. WITH THE BOUND INHIBITOR ST-17'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/2vcg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vcg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
 We synthesized biarylalanine-containing hydroxamic acids and tested them on immunoprecipitated HDAC1 and HDAC6 and show a subtype selectivity for HDAC6 that was confirmed in cells by Western blot (tubulin vs histones). We obtained an X-ray structure with a HDAC6-selective inhibitor with the bacterial deacetylase HDAH. Docking studies were carried out using HDAC1 and HDAC6 protein models. Antiproliferative activity was shown on cancer cells for selected compounds.
-==About this Structure==
+Phenylalanine-containing hydroxamic acids as selective inhibitors of class IIb histone deacetylases (HDACs).,Schafer S, Saunders L, Eliseeva E, Velena A, Jung M, Schwienhorst A, Strasser A, Dickmanns A, Ficner R, Schlimme S, Sippl W, Verdin E, Jung M Bioorg Med Chem. 2008 Feb 15;16(4):2011-33. Epub 2007 Nov 4. PMID:18054239<ref>PMID:18054239</ref>
-VCG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp. Alcaligenes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VCG OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Phenylalanine-containing hydroxamic acids as selective inhibitors of class IIb histone deacetylases (HDACs)., Schafer S, Saunders L, Eliseeva E, Velena A, Jung M, Schwienhorst A, Strasser A, Dickmanns A, Ficner R, Schlimme S, Sippl W, Verdin E, Jung M, Bioorg Med Chem. 2008 Feb 15;16(4):2011-33. Epub 2007 Nov 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18054239 18054239]
+</div>
-[[Category: Alcaligenes sp.]]
+<div class="pdbe-citations 2vcg" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
-[[Category: Dickmanns, A.]]
-[[Category: Ficner, R.]]
-[[Category: Strasser, A.]]
-[[Category: hdac-like amidohydrolase]]
-[[Category: hdah]]
-[[Category: histone deacetylase-like amidohydrolase]]
-[[Category: hydrolase]]
-[[Category: inhibitor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:10:56 2008''
+==See Also==
+*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Alcaligenes sp]]
+[[Category: Large Structures]]
+[[Category: Dickmanns A]]
+[[Category: Ficner R]]
+[[Category: Strasser A]]

2vcg

From Proteopedia

Current revision

Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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