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.


2v5w

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:06, 13 December 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of HDAC8-substrate complex==
==Crystal structure of HDAC8-substrate complex==
-
<StructureSection load='2v5w' size='340' side='right' caption='[[2v5w]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+
<StructureSection load='2v5w' size='340' side='right'caption='[[2v5w]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[2v5w]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V5W FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[2v5w]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V5W FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+
</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&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=MCM:7-AMINO-4-METHYL-CHROMEN-2-ONE'>MCM</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MCM:7-AMINO-4-METHYL-CHROMEN-2-ONE'>MCM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1t64|1t64]], [[1t67|1t67]], [[1t69|1t69]], [[1vkg|1vkg]], [[1w22|1w22]], [[2v5x|2v5x]]</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=2v5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v5w OCA], [https://pdbe.org/2v5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v5w RCSB], [https://www.ebi.ac.uk/pdbsum/2v5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v5w ProSAT]</span></td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v5w RCSB], [http://www.ebi.ac.uk/pdbsum/2v5w PDBsum]</span></td></tr>
+
</table>
-
<table>
+
== Function ==
 +
[https://www.uniprot.org/uniprot/HDAC8_HUMAN HDAC8_HUMAN] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. May play a role in smooth muscle cell contractility.<ref>PMID:10748112</ref> <ref>PMID:10926844</ref> <ref>PMID:10922473</ref> <ref>PMID:14701748</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
<jmolCheckbox>
<jmolCheckbox>
-
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v5/2v5w_consurf.spt"</scriptWhenChecked>
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v5/2v5w_consurf.spt"</scriptWhenChecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata ConSurf].
+
</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=2v5w ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
Line 26: Line 28:
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
 +
<div class="pdbe-citations 2v5w" style="background-color:#fffaf0;"></div>
==See Also==
==See Also==
-
*[[Histone deacetylase|Histone deacetylase]]
+
*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
== References ==
== References ==
<references/>
<references/>
Line 34: Line 37:
</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Carfi, A.]]
+
[[Category: Large Structures]]
-
[[Category: Defrancesco, R.]]
+
[[Category: Synthetic construct]]
-
[[Category: Gallinari, P.]]
+
[[Category: Di Marco S]]
-
[[Category: Jones, P.]]
+
[[Category: Vannini A]]
-
[[Category: Marco, S Di.]]
+
[[Category: Volpari C]]
-
[[Category: Mattu, M.]]
+
-
[[Category: Steinkuhler, C.]]
+
-
[[Category: Vannini, A.]]
+
-
[[Category: Volpari, C.]]
+
-
[[Category: Chromatin]]
+
-
[[Category: Chromatin regulator]]
+
-
[[Category: Deacetylation]]
+
-
[[Category: Hdac]]
+
-
[[Category: Hdac8]]
+
-
[[Category: Histone deacetylase]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Hydrolase-hydrolase substrate complex]]
+
-
[[Category: Nuclear protein]]
+
-
[[Category: Nucleus]]
+
-
[[Category: P53]]
+
-
[[Category: Peptidic substrate]]
+
-
[[Category: Repressor]]
+
-
[[Category: Transcription]]
+
-
[[Category: Transcription regulation]]
+

Current revision

Crystal structure of HDAC8-substrate complex

PDB ID 2v5w

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/2v5w"
Personal tools