Histone deacetylase 3D structures: Difference between revisions

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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|
{{#tree:id=OrganizedByTopic|openlevels=0|
*'''HDAC class I'''
*'''HDAC class I'''
*HDAC1
*HDAC1
**[[4bkx]] – hHDAC1 + MTA1 – human<br />
**[[4bkx]] – hHDAC1 + MTA1 – human<br />
**[[3hgq]], [[3hgt]] – hHDAC1 subunit 3<br />
**[[3hgq]], [[3hgt]] – hHDAC1 subunit 3<br />
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**[[5j8j]] – yHDAC1 residues 457-698 – yeast<br />
**[[5j8j]] – yHDAC1 residues 457-698 – yeast<br />
**[[6z6f]], [[6z6h]], [[6z6o]], [[6z6p]] – yHDAC1 – Cryo EM<br />
**[[6z6f]], [[6z6h]], [[6z6o]], [[6z6p]] – yHDAC1 – Cryo EM<br />
*HDAC2
*HDAC2
**[[3max]] – hHDAC2 + amide derivative <br />
**[[3max]] – hHDAC2 + amide derivative <br />
**[[4lxz]], [[6g3o]] – hHDAC2 core domain + SAHA<br />
**[[4lxz]], [[6g3o]] – hHDAC2 core domain + SAHA<br />
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**[[7vmf]], [[7vmh]] – AtHDAC2d residues 1-95 <br />
**[[7vmf]], [[7vmh]] – AtHDAC2d residues 1-95 <br />
**[[7vmi]] – AtHDAC2c residues 1-95 <br />
**[[7vmi]] – AtHDAC2c residues 1-95 <br />
*HDAC3
*HDAC3
**[[4a69]] – hHDAC3 + nuclear receptor corepressor 2 + inositol tetraphosphate
**[[4a69]] – hHDAC3 + nuclear receptor corepressor 2 + inositol tetraphosphate
*HDAC8
*HDAC8
**[[3ew8]], [[3ezp]], [[3ezt]], [[3f06]] – hHDAC8 (mutant)<br />  
**[[3ew8]], [[3ezp]], [[3ezt]], [[3f06]] – hHDAC8 (mutant)<br />  
**[[3sff]], [[3sfh]] – hHDAC8 + inhibitor<br />
**[[3sff]], [[3sfh]] – hHDAC8 + inhibitor<br />
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**[[4bz6]], [[6fu1]], [[6gx3]], [[6gxa]], [[6gxu]], [[6gxw]] – SmHDAC8 + SAHA  
**[[4bz6]], [[6fu1]], [[6gx3]], [[6gxa]], [[6gxu]], [[6gxw]] – SmHDAC8 + SAHA  
derivative<br />
derivative<br />
*HDAC Rpd3
*HDAC Rpd3
**[[8kc7]], [[8w9c]] – yRpd3 + SIN3 + RCO1 + EAF3 – Cryo EM<br />
**[[8kc7]], [[8w9c]] – yRpd3 + SIN3 + RCO1 + EAF3 – Cryo EM<br />
**[[8hxx]] – yRpd3 + SIN3 + RCO1 + EAF3 + histone H3 – Cryo EM<br />
**[[8hxx]] – yRpd3 + SIN3 + RCO1 + EAF3 + histone H3 – Cryo EM<br />
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**[[8hpo]] – yRpd3 in SIN3/HDAC complex – Cryo EM<br />
**[[8hpo]] – yRpd3 in SIN3/HDAC complex – Cryo EM<br />
**[[8ga8]] – yRpd3 in Rpd3L complex – Cryo EM<br />
**[[8ga8]] – yRpd3 in Rpd3L complex – Cryo EM<br />
*HDAC Clr
*HDAC Clr
**[[5ikk]] – fyClr3 – fission yeast<br />
**[[5ikk]] – fyClr3 – fission yeast<br />
**[[8ifg]] – fyClr6 + Prw1 + Pst2 + Eaf3 + Cph1 + Cph2 – Cryo EM<br />
**[[8ifg]] – fyClr6 + Prw1 + Pst2 + Eaf3 + Cph1 + Cph2 – Cryo EM<br />
**[[8i03]] – fyClr6 in SIN3L complex – Cryo EM<br />
**[[8i03]] – fyClr6 in SIN3L complex – Cryo EM<br />
*'''HDAC class IIA'''
*'''HDAC class IIA'''
*HDAC4
*HDAC4
**[[2h8n]] – hHDAC4 N terminal <br />
**[[2h8n]] – hHDAC4 N terminal <br />
**[[2o94]] - hHDAC4 N terminal (mutant)<br />
**[[2o94]] - hHDAC4 N terminal (mutant)<br />
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**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor<br />
**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor<br />
**[[5zop]], [[5zoo]] - hHDAC4 catalytic domain (mutant) + SMRT corepressor<br />
**[[5zop]], [[5zoo]] - hHDAC4 catalytic domain (mutant) + SMRT corepressor<br />
*HDAC5
*HDAC5
**[[5uwi]] – hHDAC5 + RAN + RANBP1 + exportin<br />
**[[5uwi]] – hHDAC5 + RAN + RANBP1 + exportin<br />
*HDAC7
*HDAC7
**[[3c0y]] – hHDAC7 catalytic domain<br />
**[[3c0y]] – hHDAC7 catalytic domain<br />
**[[3c0z]] - hHDAC7 catalytic domain + octanedioic acid hydroxyamide phenylamide<br />
**[[3c0z]] - hHDAC7 catalytic domain + octanedioic acid hydroxyamide phenylamide<br />
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**[[3znr]], [[3zns]] - hHDAC7 catalytic domain + inhibitor<br />
**[[3znr]], [[3zns]] - hHDAC7 catalytic domain + inhibitor<br />
**[[8wzl]] – AtHDAC7 8-383<br />
**[[8wzl]] – AtHDAC7 8-383<br />
*HDAC9
*HDAC9
**[[1tqe]] – mHDAC9 + myocyte-specific enhancer factor + DNA – mouse
**[[1tqe]] – mHDAC9 + myocyte-specific enhancer factor + DNA – mouse
*HDAC10 or polyamine deacetylase 10
*HDAC10 or polyamine deacetylase 10
**[[5td7]], [[7kuv]] – zHDAC10 - zebrafish<br />
**[[5td7]], [[7kuv]] – zHDAC10 - zebrafish<br />
**[[6ufn]], [[6ufo]], [[6uhu]], [[6uhv]], [[6uii]], [[6uij]], [[6uil]], [[6uim]], [[6wbq]], [[6wdv]], [[6wdw]], [[6wdx]], [[6wdy]], [[7sgg]], [[7sgi]], [[7sgj]], [[7sgk]], [[7u3m]], [[7u59]], [[7u69]], [[7u6a]], [[7u6b]], [[9cbf]], [[9cbg]], [[9cbh]], [[9cbi]] – zHDAC10 + inhibitor<br />
**[[6ufn]], [[6ufo]], [[6uhu]], [[6uhv]], [[6uii]], [[6uij]], [[6uil]], [[6uim]], [[6wbq]], [[6wdv]], [[6wdw]], [[6wdx]], [[6wdy]], [[7sgg]], [[7sgi]], [[7sgj]], [[7sgk]], [[7u3m]], [[7u59]], [[7u69]], [[7u6a]], [[7u6b]], [[9cbf]], [[9cbg]], [[9cbh]], [[9cbi]] – zHDAC10 + inhibitor<br />
**[[6vnq]], [[7kuq]], [[7kur]], [[7kus]], [[7kut]] – zHDAC10 (mutant) + inhibitor <br />
**[[6vnq]], [[7kuq]], [[7kur]], [[7kus]], [[7kut]] – zHDAC10 (mutant) + inhibitor <br />
*HDAC
*HDAC
**[[4a6q]], [[4a90]] - hHDAC subunit SAP18 <br />
**[[4a6q]], [[4a90]] - hHDAC subunit SAP18 <br />
**[[2hde]] – hHDAC subunit SAP18 (mutant) – NMR<br />
**[[2hde]] – hHDAC subunit SAP18 (mutant) – NMR<br />
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**[[9gky]] – VcHDAC + decanoic acid – ''Vibrio cholerae''<br />
**[[9gky]] – VcHDAC + decanoic acid – ''Vibrio cholerae''<br />
**[[9gkv]] – VcHDAC + SAHA<br />
**[[9gkv]] – VcHDAC + SAHA<br />
*'''HDAC class IIB'''
*'''HDAC class IIB'''
*HDAC6; ; Domains – catalytic 2 288-646; CD1 – 40-440; CD2  440-798; zinc finger 1109-1213
*HDAC6; ; Domains – catalytic 2 288-646; CD1 – 40-440; CD2  440-798; zinc finger 1109-1213
**[[3c5k]] – hHDAC6 zinc finger domain<br />
**[[3c5k]] – hHDAC6 zinc finger domain<br />
**[[3gv4]] - hHDAC6 zinc finger domain + ubiquitin peptide<br />
**[[3gv4]] - hHDAC6 zinc finger domain + ubiquitin peptide<br />
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**[[53fj]], [[5efk]], [[5efn]] – zHDAC6 catalytic domain (mutant) + peptide <br />
**[[53fj]], [[5efk]], [[5efn]] – zHDAC6 catalytic domain (mutant) + peptide <br />
**[[8a8z]] – zHDAC6 CD2 domain 440-798 + inhibitor <br />
**[[8a8z]] – zHDAC6 CD2 domain 440-798 + inhibitor <br />
*HDAC15
*HDAC15
**[[6j6t]] – AtHDAC15 HD domain <br />
**[[6j6t]] – AtHDAC15 HD domain <br />
*'''HDAC class III'''
*'''HDAC class III'''
*SIRT1 or NAD-dependent protein deacetylase sirtuin-1
*SIRT1 or NAD-dependent protein deacetylase sirtuin-1
**[[4ig9]] – hSIRT1 + Zn<br />
**[[4ig9]] – hSIRT1 + Zn<br />
**[[4i5i]] – hSIRT1 + NAD + indole + Zn<br />
**[[4i5i]] – hSIRT1 + NAD + indole + Zn<br />
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**[[4zzi]] – hSIRT1 + activator + inhibitor + Zn<br />
**[[4zzi]] – hSIRT1 + activator + inhibitor + Zn<br />
**[[4zzj]] – hSIRT1 + acetyl lysine peptide + activator + Zn<br />
**[[4zzj]] – hSIRT1 + acetyl lysine peptide + activator + Zn<br />
*SIRT2
*SIRT2
**[[1j8f]], [[3zgo]], [[9s44]] – hSIRT2 + Zn<br />
**[[1j8f]], [[3zgo]], [[9s44]] – hSIRT2 + Zn<br />
**[[5yqo]], [[5yqn]], [[5yqm]], [[5yql]] – hSIRT2 + inhibitor + Zn<br />
**[[5yqo]], [[5yqn]], [[5yqm]], [[5yql]] – hSIRT2 + inhibitor + Zn<br />
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**[[2hjh]] – ySIRT2 + pseudosubstrate + nicotinamide + Zn <br />
**[[2hjh]] – ySIRT2 + pseudosubstrate + nicotinamide + Zn <br />
**[[4iao]] – ySIRT2 + SIRT4 + ADP-ribose + Zn<br />
**[[4iao]] – ySIRT2 + SIRT4 + ADP-ribose + Zn<br />
*SIRT3
*SIRT3
**[[5d7n]] – hSIRT3 + Zn<br />
**[[5d7n]] – hSIRT3 + Zn<br />
**[[3gls]] – hSIRT3 (mutant) + Zn<br />
**[[3gls]] – hSIRT3 (mutant) + Zn<br />
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**[[4bvf]], [[4bvg]] – hSIRT3 + acetyl lysine peptide + inhibitor + Zn<br />
**[[4bvf]], [[4bvg]] – hSIRT3 + acetyl lysine peptide + inhibitor + Zn<br />
**[[5h4d]] – hSIRT3 + agonist + NAD + Zn<br/ >
**[[5h4d]] – hSIRT3 + agonist + NAD + Zn<br/ >
*SIRT4
*SIRT4
**[[5ojn]] – hSIRT4 + ADP-ribose  + Zn – ''Xenopus tropicalis''<br />
**[[5ojn]] – hSIRT4 + ADP-ribose  + Zn – ''Xenopus tropicalis''<br />
*SIRT5
*SIRT5
**[[2b4y]], [[4bn4]] – hSIRT5 + ADP-ribose + Zn<br />
**[[2b4y]], [[4bn4]] – hSIRT5 + ADP-ribose + Zn<br />
**[[2nyr]], [[5xhs]] – hSIRT5 + inhibitor + Zn<br />
**[[2nyr]], [[5xhs]] – hSIRT5 + inhibitor + Zn<br />
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**[[6enx]], [[6eo0]], [[6eqs]] – zSIRT5 + inhibitor + Zn <br />
**[[6enx]], [[6eo0]], [[6eqs]] – zSIRT5 + inhibitor + Zn <br />
**[[5ojo]] – zSIRT5 + CPS1 peptide + Zn <br />
**[[5ojo]] – zSIRT5 + CPS1 peptide + Zn <br />
*SIRT6
*SIRT6
**[[3k35]], [[6xuy]], [[6xv6]] – hSIRT6 + ADP-ribose + Zn<br />
**[[3k35]], [[6xuy]], [[6xv6]] – hSIRT6 + ADP-ribose + Zn<br />
**[[5x16]] – hSIRT6 + oxolan derivative + Zn<br />
**[[5x16]] – hSIRT6 + oxolan derivative + Zn<br />
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**[[5mfz]], [[5mfp]], [[5mf6]], [[5mgn]], [[6xv1]], [[6xvg]], [[6zu4]] – hSIRT6 + activator + Zn<br />
**[[5mfz]], [[5mfp]], [[5mf6]], [[5mgn]], [[6xv1]], [[6xvg]], [[6zu4]] – hSIRT6 + activator + Zn<br />
**[[5y2f]], [[7cl0]], [[7cl1]] – hSIRT6 + peptide activator + Zn<br />
**[[5y2f]], [[7cl0]], [[7cl1]] – hSIRT6 + peptide activator + Zn<br />
*SIRT7
*SIRT7
**[[5iqz]] – hSIRT7 N-terminal<br />
**[[5iqz]] – hSIRT7 N-terminal<br />
*HDAC-like
*HDAC-like
**[[1zz0]], [[5g1b]] – AbHDAH – ''Alcalifenaceae bacterium''<br />
**[[1zz0]], [[5g1b]] – AbHDAH – ''Alcalifenaceae bacterium''<br />
**[[1zz3]], [[2gh6]], [[2vcg]], [[5g1a]], [[5g1c]], [[5g3w]] – AbHDAH + inhibitor <br />
**[[1zz3]], [[2gh6]], [[2vcg]], [[5g1a]], [[5g1c]], [[5g3w]] – AbHDAH + inhibitor <br />

Revision as of 09:42, 29 March 2026

3D Structures of histone deacetylase

Updated on 29-March-2026

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Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Openfox

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