Histone deacetylase 3D structures: Difference between revisions

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*'''HDAC class I'''

*HDAC1

**[[4bkx]] – hHDAC1 + MTA1 – human<br />

**[[3hgq]], [[3hgt]] – hHDAC1 subunit 3<br />

**[[5j8j]] – yHDAC1 residues 457-698 – yeast<br />

**[[6z6f]], [[6z6h]], [[6z6o]], [[6z6p]] – yHDAC1 – Cryo EM<br />

*HDAC2

**[[3max]] – hHDAC2 + amide derivative <br />

**[[4lxz]], [[6g3o]] – hHDAC2 core domain + SAHA<br />

**[[7vmf]], [[7vmh]] – AtHDAC2d residues 1-95 <br />

**[[7vmi]] – AtHDAC2c residues 1-95 <br />

*HDAC3

**[[4a69]] – hHDAC3 + nuclear receptor corepressor 2 + inositol tetraphosphate

*HDAC8

**[[3ew8]], [[3ezp]], [[3ezt]], [[3f06]] – hHDAC8 (mutant)<br />  

**[[3sff]], [[3sfh]] – hHDAC8 + inhibitor<br />

**[[4bz6]], [[6fu1]], [[6gx3]], [[6gxa]], [[6gxu]], [[6gxw]] – SmHDAC8 + SAHA  

derivative<br />

*HDAC Rpd3

**[[8kc7]], [[8w9c]] – yRpd3 + SIN3 + RCO1 + EAF3 – Cryo EM<br />

**[[8hxx]] – yRpd3 + SIN3 + RCO1 + EAF3 + histone H3 – Cryo EM<br />

**[[8hpo]] – yRpd3 in SIN3/HDAC complex – Cryo EM<br />

**[[8ga8]] – yRpd3 in Rpd3L complex – Cryo EM<br />

*HDAC Clr

**[[5ikk]] – fyClr3 – fission yeast<br />

**[[8ifg]] – fyClr6 + Prw1 + Pst2 + Eaf3 + Cph1 + Cph2 – Cryo EM<br />

**[[8i03]] – fyClr6 in SIN3L complex – Cryo EM<br />

*'''HDAC class IIA'''

*HDAC4

**[[2h8n]] – hHDAC4 N terminal <br />

**[[2o94]] - hHDAC4 N terminal (mutant)<br />

**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor<br />

**[[5zop]], [[5zoo]] - hHDAC4 catalytic domain (mutant) + SMRT corepressor<br />

*HDAC5

**[[5uwi]] – hHDAC5 + RAN + RANBP1 + exportin<br />

*HDAC7

**[[3c0y]] – hHDAC7 catalytic domain<br />

**[[3c0z]] - hHDAC7 catalytic domain + octanedioic acid hydroxyamide phenylamide<br />

**[[3znr]], [[3zns]] - hHDAC7 catalytic domain + inhibitor<br />

**[[8wzl]] – AtHDAC7 8-383<br />

*HDAC9

**[[1tqe]] – mHDAC9 + myocyte-specific enhancer factor + DNA – mouse

*HDAC10 or polyamine deacetylase 10

**[[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 />

**[[6vnq]], [[7kuq]], [[7kur]], [[7kus]], [[7kut]] – zHDAC10 (mutant) + inhibitor <br />

*HDAC

**[[4a6q]], [[4a90]] - hHDAC subunit SAP18 <br />

**[[2hde]] – hHDAC subunit SAP18 (mutant) – NMR<br />

**[[9gky]] – VcHDAC + decanoic acid – ''Vibrio cholerae''<br />

**[[9gkv]] – VcHDAC + SAHA<br />

*'''HDAC class IIB'''

*HDAC6; ; Domains – catalytic 2 288-646; CD1 – 40-440; CD2  440-798; zinc finger 1109-1213

**[[3c5k]] – hHDAC6 zinc finger domain<br />

**[[3gv4]] - hHDAC6 zinc finger domain + ubiquitin peptide<br />

**[[53fj]], [[5efk]], [[5efn]] – zHDAC6 catalytic domain (mutant) + peptide <br />

**[[8a8z]] – zHDAC6 CD2 domain 440-798 + inhibitor <br />

*HDAC15

**[[6j6t]] – AtHDAC15 HD domain <br />

*'''HDAC class III'''

*SIRT1 or NAD-dependent protein deacetylase sirtuin-1

**[[4ig9]] – hSIRT1 + Zn<br />

**[[4i5i]] – hSIRT1 + NAD + indole + Zn<br />

**[[4zzi]] – hSIRT1 + activator + inhibitor + Zn<br />

**[[4zzj]] – hSIRT1 + acetyl lysine peptide + activator + Zn<br />

*SIRT2

**[[1j8f]], [[3zgo]], [[9s44]] – hSIRT2 + Zn<br />

**[[5yqo]], [[5yqn]], [[5yqm]], [[5yql]] – hSIRT2 + inhibitor + Zn<br />

**[[2hjh]] – ySIRT2 + pseudosubstrate + nicotinamide + Zn <br />

**[[4iao]] – ySIRT2 + SIRT4 + ADP-ribose + Zn<br />

*SIRT3

**[[5d7n]] – hSIRT3 + Zn<br />

**[[3gls]] – hSIRT3 (mutant) + Zn<br />

**[[4bvf]], [[4bvg]] – hSIRT3 + acetyl lysine peptide + inhibitor + Zn<br />

**[[5h4d]] – hSIRT3 + agonist + NAD + Zn<br/ >

*SIRT4

**[[5ojn]] – hSIRT4 + ADP-ribose  + Zn – ''Xenopus tropicalis''<br />

*SIRT5

**[[2b4y]], [[4bn4]] – hSIRT5 + ADP-ribose + Zn<br />

**[[2nyr]], [[5xhs]] – hSIRT5 + inhibitor + Zn<br />

**[[6enx]], [[6eo0]], [[6eqs]] – zSIRT5 + inhibitor + Zn <br />

**[[5ojo]] – zSIRT5 + CPS1 peptide + Zn <br />

*SIRT6

**[[3k35]], [[6xuy]], [[6xv6]] – hSIRT6 + ADP-ribose + Zn<br />

**[[5x16]] – hSIRT6 + oxolan derivative + Zn<br />

**[[5mfz]], [[5mfp]], [[5mf6]], [[5mgn]], [[6xv1]], [[6xvg]], [[6zu4]] – hSIRT6 + activator + Zn<br />

**[[5y2f]], [[7cl0]], [[7cl1]] – hSIRT6 + peptide activator + Zn<br />

*SIRT7

**[[5iqz]] – hSIRT7 N-terminal<br />

*HDAC-like

**[[1zz0]], [[5g1b]] – AbHDAH – ''Alcalifenaceae bacterium''<br />

**[[1zz3]], [[2gh6]], [[2vcg]], [[5g1a]], [[5g1c]], [[5g3w]] – AbHDAH + inhibitor <br />