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Histone deacetylase 3D structures

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(New page: == 3D Structures of histone deacetylase == Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} {{#tree:id=OrganizedByTopic|openlevels=0| *'''HDAC class I''' *HD...)
Current revision (07:23, 22 May 2023) (edit) (undo)
 
(5 intermediate revisions not shown.)
Line 11: Line 11:
**[[3hgq]], [[3hgt]] – hHDAC1 subunit 3<br />
**[[3hgq]], [[3hgt]] – hHDAC1 subunit 3<br />
**[[5icn]] – hHDAC1 + MTA1 + peptide<br />
**[[5icn]] – hHDAC1 + MTA1 + peptide<br />
 +
**[[7ao8]], [[7ao9]] – hHDAC1 + MTA1 + MBD2 – Cryo EM<br />
 +
**[[7aoa]] – hHDAC1 + MTA1 + MBD2 + RBBP4 – Cryo EM<br />
 +
**[[6z2j]], [[6z2k]] – hHDAC1 + DNTTIP1 + Midac deacetylase – Cryo EM<br />
**[[5j8j]] – yHDAC1 residues 457-698 – yeast<br />
**[[5j8j]] – yHDAC1 residues 457-698 – yeast<br />
 +
**[[6z6f]], [[6z6h]], [[6z6o]], [[6z6p]] – yHDAC1 – Cryo EM<br />
*HDAC2
*HDAC2
**[[3max]] – hHDAC2 + amide derivative <br />
**[[3max]] – hHDAC2 + amide derivative <br />
-
**[[4lxz]] – hHDAC2 core domain + SAHA<br />
+
**[[4lxz]], [[6g3o]] – hHDAC2 core domain + SAHA<br />
-
**[[4ly1]], [[5iwg]], [[5ix0]] – hHDAC2 core domain + inhibitor<br />
+
**[[8bpa]], [[8bpb]], [[8c60]] – hHDAC2 + SIN3B + PF1 – Cryo EM<br />
 +
**[[8bpc]] – hHDAC2 + SIN3B + PF1 + SAHA – Cryo EM<br />
 +
**[[8bpa]], [[8bpb]], [[8c60]] – hHDAC2 + SIN3B + PF1 – Cryo EM<br />
 +
**[[8bpc]] – hHDAC2 + SIN3B + PF1 + SAHA – Cryo EM<br />
 +
**[[4ly1]], [[5iwg]], [[5ix0]], [[6wbz]], [[6wbw]], [[6xdm]], [[6xeb]], [[6xec]], [[7js8]], [[7kbh]], [[7kbg]], [[7ltg]], [[7ltk]], [[7ltl]], [[7mot]], [[7mox]], [[7moy]], [[7zzo]], [[7zzp]], [[7zzr]], [[7zzs]], [[7zzt]], [[7zzv]], [[7zzw]], [[8a0b]] – hHDAC2 core domain + inhibitor<br />
 +
**[[6whn]], [[6who]], [[6whq]], [[6whz]], [[6wi3]], [[7mos]], [[7moz]] – hHDAC2 core domain + peptide macrocycle<br />
 +
**[[7vrr]] – AtHDAC2a residues 1-95 – ''Arabidopsis thaliana''<br />
 +
**[[7vmf]], [[7vmh]] – AtHDAC2d residues 1-95 <br />
 +
**[[7vmi]] – AtHDAC2c residues 1-95 <br />
*HDAC3
*HDAC3
Line 27: Line 39:
**[[3ew8]], [[3ezp]], [[3ezt]], [[3f06]] – hHDAC8 (mutant)<br />
**[[3ew8]], [[3ezp]], [[3ezt]], [[3f06]] – hHDAC8 (mutant)<br />
**[[3sff]], [[3sfh]] – hHDAC8 + inhibitor<br />
**[[3sff]], [[3sfh]] – hHDAC8 + inhibitor<br />
 +
**[[4qa1]], [[4qa2]], [[4qa3]], [[4qa4]] - hHDAC8 (mutant) + inhibitor<br />
**[[1t64]], [[3f0r]], [[5ths]] – hHDAC8 + trichostatin A <br />
**[[1t64]], [[3f0r]], [[5ths]] – hHDAC8 + trichostatin A <br />
-
**[[5tht]], [[5thu]], [[5thv]], [[5dc5]], [[5d1b]] - hHDAC8 (mutant) + amide derivative<br />
+
**[[5tht]], [[5thu]], [[5thv]], [[5dc5]], [[5d1b]], [[7jvw]] - hHDAC8 (mutant) + amide derivative<br />
-
**[[1t67]], [[1w22]], [[1vkg]], [[3f07]] - hHDAC8 + amide derivative<br />
+
**[[1t67]], [[1w22]], [[1vkg]], [[3f07]], [[6oda]], [[6odb]], [[6odc]] - hHDAC8 + amide derivative<br />
**[[1t69]] - hHDAC8 + SAHA<br />
**[[1t69]] - hHDAC8 + SAHA<br />
-
**[[4qa0]] - hHDAC8 (mutant) + SAHA<br />
+
**[[4qa0]], [[7jvu]] - hHDAC8 (mutant) + SAHA<br />
**[[5fcw]], [[5fue]] - hHDAC8 + hydroxamate<br />
**[[5fcw]], [[5fue]] - hHDAC8 + hydroxamate<br />
**[[5vi6]] - hHDAC8 + trapoxin A<br />
**[[5vi6]] - hHDAC8 + trapoxin A<br />
-
**[[4qa1]], [[4qa2]], [[4qa3]], [[4qa4]] - hHDAC8 (mutant) + inhibitor<br />
 
**[[2v5w]] – hHDAC8 + tripeptide substrate<br />
**[[2v5w]] – hHDAC8 + tripeptide substrate<br />
-
**[[4qa5]], [[4qa6]], [[4qa7]], [[3ewf]], [[5dc8]], [[5dc7]], [[5dc6]], [[5d1d]], [[5d1c]] - hHDAC8 (mutant) + tetrapeptide substrate<br />
+
**[[4qa5]], [[4qa6]], [[4qa7]], [[3ewf]], [[5dc8]], [[5dc7]], [[5dc6]], [[5d1d]], [[5d1c]], [[7jvv]], [[7p3s]] - hHDAC8 (mutant) + tetrapeptide substrate<br />
**[[3rqd]] - hHDAC8 + largazole<br />
**[[3rqd]] - hHDAC8 + largazole<br />
**[[4rn0]], [[4rn1]], [[4rn2]] - hHDAC8 (mutant) + largazole analog<br />
**[[4rn0]], [[4rn1]], [[4rn2]] - hHDAC8 (mutant) + largazole analog<br />
Line 46: Line 58:
**[[2v5x]] - hHDAC8 (mutant) + octanediamide derivative<br />
**[[2v5x]] - hHDAC8 (mutant) + octanediamide derivative<br />
**[[4bz5]] – SmHDAC8 – ''Schistosoma mansoni''<br />
**[[4bz5]] – SmHDAC8 – ''Schistosoma mansoni''<br />
-
**[[4bz7]], [[4bz8]], [[4bz9]], [[4cqf]], [[6hsz]], [[6ht8]], [[6htg]], [[6hth]], [[6hti]], [[6htt]], [[6htz]], [[6hu0]], [[6hu1]], [[6hu2]], [[6hu3]], [[6hsh]], [[6hrq]], [[6hqy]] – SmHDAC8 + inhibitor<br />
+
**[[4bz7]], [[4bz8]], [[4bz9]], [[4cqf]], [[6hsz]], [[6ht8]], [[6htg]], [[6hth]], [[6hti]], [[6htt]], [[6htz]], [[6hu0]], [[6hu1]], [[6hu2]], [[6hu3]], [[6hsh]], [[6hrq]], [[6hqy]], [[6tld]], [[7p2s]], [[7p2t]], [[7p2u]], [[7p2v]], [[7p3s]], [[7poz]] – SmHDAC8 + inhibitor<br />
**[[6hsk]], [[6hsf]], [[6hsg]] – SmHDAC8 (mutant) + inhibitor<br />
**[[6hsk]], [[6hsf]], [[6hsg]] – SmHDAC8 (mutant) + inhibitor<br />
**[[4bz6]], [[6gxw]], [[6gxu]], [[6gxa]], [[6gx3]], [[6fu1]] – SmHDAC8 + SAHA derivative<br />
**[[4bz6]], [[6gxw]], [[6gxu]], [[6gxa]], [[6gx3]], [[6fu1]] – SmHDAC8 + SAHA derivative<br />
Line 76: Line 88:
**[[1tqe]] – mHDAC9 + myocyte-specific enhancer factor + DNA – mouse
**[[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]] – zHDAC10 + inhibitor<br />
 +
**[[6vnq]], [[7kuq]], [[7kur]], [[7kus]], [[7kut]] – zHDAC10 (mutant) + inhibitor <br />
*HDAC
*HDAC
Line 85: Line 103:
**[[2ld7]] – hHDAC subunit SAP30 +SIN3A PAH 3 domain – NMR<br />
**[[2ld7]] – hHDAC subunit SAP30 +SIN3A PAH 3 domain – NMR<br />
**[[5ikk]] – HDAC CLR3 – fission yeast<br />
**[[5ikk]] – HDAC CLR3 – fission yeast<br />
 +
**[[7q1b]], [[7q1c]] – HDAC DAC2 + inhibitor – ''Trypanosoma cruzi''<br />
*'''HDAC class IIB'''
*'''HDAC class IIB'''
-
*HDAC6
+
*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 />
**[[3phd]] - hHDAC6 + polyubiquitin<br />
**[[3phd]] - hHDAC6 + polyubiquitin<br />
-
**[[5kh3]], [[5kh7]], [[5kh9]], [[5b8d]], [[6ce6]], [[6ce8]], [[6cea]], [[6cec]], [[6ced]], [[6cee]], [[6cef]], [[5wpb]], [[5wbn]] – hHDAC6 zinc finger + inhibitor<br />
+
**[[5kh3]], [[5kh7]], [[5kh9]], [[5b8d]], [[6ce6]], [[6ce8]], [[6cea]], [[6cec]], [[6ced]], [[6cee]], [[6cef]], [[5wpb]], [[5wbn]], [[8g43]], [[8g44]], [[8g45]] – hHDAC6 zinc finger + inhibitor<br />
-
**[[5eem]] – zHDAC6 catalytic domain - zebrafish<br />
+
**[[7qno]] – zHDAC6 CD1+CD2 domain <br />
-
**[[6cgp]], [[5wgm]], [[5wgl]], [[5wgi]], [[5wgk]], [[5g0j]], [[5g0i]], [[5g0h]], [[5g0g]], [[5g0f]], [[5efh]], [[5efg]], [[5efb]], [[5ef7]], [[5ef8]], [[5een]], [[5eek]], [[5eef]], [[6mr5]], [[6dvo]], [[6dvn]], [[6dvm]], [[6dvl]], [[6cw8]] – zHDAC6 catalytic domain + inhibitor <br />
+
**[[5eem]] – zHDAC6 catalytic domain<br />
 +
**[[5edu]], [[6cgp]], [[5wgm]], [[5wgl]], [[5wgi]], [[5wgk]], [[5g0j]], [[5g0i]], [[5g0h]], [[5g0g]], [[5g0f]], [[5efh]], [[5efg]], [[5efb]], [[5ef7]], [[5ef8]], [[5een]], [[5eek]], [[5eef]], [[6mr5]], [[6dvo]], [[6dvn]], [[6dvm]], [[6dvl]], [[6cw8]], [[6pye]], [[6pzo]], [[6pzr]], [[6pzs]], [[6pzu]], [[6q0z]], [[6r0k]], [[6tcy]], [[6thv]], [[6uo2]], [[6uo3]], [[6uo5]], [[6uo7]], [[6v79]], [[6v7a]], [[6vnr]], [[6zw1]], [[7jom]], [[7o2p]], [[7o2r]], [[7u8z]], [[7uk2]], [[8d98]], [[8d99]], [[8d9a]], [[8d9b]], [[8d9c]] – zHDAC6 catalytic domain 2 + inhibitor <br />
 +
**[[6uo4]], [[6uo7]], [[6uob]], [[6uoc]], [[6wyo]] – zHDAC6 catalytic domain (mutant) + inhibitor <br />
**[[5eei]], [[6css]], [[6csr]], [[6csq]], [[6csp]], [[5w5k]] – zHDAC6 catalytic domain + SAHA derivative<br />
**[[5eei]], [[6css]], [[6csr]], [[6csq]], [[6csp]], [[5w5k]] – zHDAC6 catalytic domain + SAHA derivative<br />
 +
**[[6wyp]], [[6wyq]] – zHDAC6 catalytic domain (mutant) + SAHA derivative<br />
 +
**[[6wsj]], [[8eqi]] – zHDAC6 catalytic domain 2 + peptide <br />
 +
**[[5efj]] – zHDAC6 catalytic domain 2 + HC toxin <br />
**[[5efn]], [[5efk]], [[53fj]] – zHDAC6 catalytic domain (mutant) + peptide <br />
**[[5efn]], [[5efk]], [[53fj]] – zHDAC6 catalytic domain (mutant) + peptide <br />
 +
**[[8a8z]] – zHDAC6 CD2 domain 440-798 + inhibitor <br />
 +
*HDAC15
 +
 +
**[[6j6t]] – AtHDAC15 HD domain <br />
*'''HDAC class III'''
*'''HDAC class III'''
-
*SIRT1
+
 
 +
*SIRT1 or NAD-dependent protein deacetylase sirtuin-1
**[[4ig9]] – hSIRT1 + Zn<br />
**[[4ig9]] – hSIRT1 + Zn<br />
Line 121: Line 150:
**[[4y6q]] – hSIRT2+ ADP ribose derivative + Zn<br />
**[[4y6q]] – hSIRT2+ ADP ribose derivative + Zn<br />
**[[4l3o]], [[4y6l]], [[4y6o]] – hSIRT2 + acetyl lysine peptide + Zn<br />
**[[4l3o]], [[4y6l]], [[4y6o]] – hSIRT2 + acetyl lysine peptide + Zn<br />
-
**[[4x3o]], [[4x3p]] – hSIRT2 + myristoyl peptide + Zn<br />
+
**[[4x3o]], [[4x3p]], [[6l65]], [[6l66]], [[6l71]], [[7bos]], [[7bot]] – hSIRT2 + myristoyl peptide + Zn<br />
-
**[[4rmg]], [[5dy4]], [[5dy5]], [[5y5n]], [[5mat]] – hSIRT2 + inhibitor + Zn<br />
+
**[[4rmg]], [[5dy4]], [[5dy5]], [[5y5n]], [[5mat]], [[6nr0]] – hSIRT2 + inhibitor + Zn<br />
 +
**[[6qcn]] – hSIRT2 + ADP-ribose + quercetin derivative + Zn<br />
**[[5d7p]], [[5d7q]], [[5mar]] – hSIRT2 + inhibitor + ADP-ribose + Zn<br />
**[[5d7p]], [[5d7q]], [[5mar]] – hSIRT2 + inhibitor + ADP-ribose + Zn<br />
**[[4rmh]], [[4rmi]] – hSIRT2 + acetyl lysine peptide + inhibitor + Zn<br />
**[[4rmh]], [[4rmi]] – hSIRT2 + acetyl lysine peptide + inhibitor + Zn<br />
Line 138: Line 168:
**[[3gls]] – hSIRT3 (mutant) + Zn<br />
**[[3gls]] – hSIRT3 (mutant) + Zn<br />
**[[3glu]], [[5ytk]], [[5y4h]] – hSIRT3 + peptide + Zn<br />
**[[3glu]], [[5ytk]], [[5y4h]] – hSIRT3 + peptide + Zn<br />
 +
**[[6iso]] – hSIRT3 + histone peptide + Zn<br />
**[[5bwo]], [[5bwn]] – hSIRT3 + palmitoyl H3K9 peptide + Zn<br />
**[[5bwo]], [[5bwn]] – hSIRT3 + palmitoyl H3K9 peptide + Zn<br />
**[[5bwl]] – hSIRT3 + succinyl peptide + Zn<br />
**[[5bwl]] – hSIRT3 + succinyl peptide + Zn<br />
Line 160: Line 191:
**[[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 />
 +
**[[6ljk]], [[6ljm]], [[6ljn]] – hSIRT5 + peptide substrate + Zn<br />
**[[3rig]], [[3riy]], [[4f4u]] – hSIRT5 + acetyl lysine peptide + Zn<br />
**[[3rig]], [[3riy]], [[4f4u]] – hSIRT5 + acetyl lysine peptide + Zn<br />
**[[4gic]] – hSIRT5 + acetyl lysine peptide + carba-NAD + Zn<br/ >
**[[4gic]] – hSIRT5 + acetyl lysine peptide + carba-NAD + Zn<br/ >
Line 171: Line 203:
*SIRT6
*SIRT6
-
**[[3k35]] – 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 />
**[[6hoy]] – hSIRT6 + ADP-ribose + trichostatin + Zn<br />
**[[6hoy]] – hSIRT6 + ADP-ribose + trichostatin + Zn<br />
 +
**[[6qcd]], [[6qce]], [[6qch]], [[6qcj]] – hSIRT6 + ADP-ribose + quercetin derivative + Zn<br />
**[[3pki]], [[3pkj]] – hSIRT6 (mutant) + ADP-ribose derivative + Zn<br />
**[[3pki]], [[3pkj]] – hSIRT6 (mutant) + ADP-ribose derivative + Zn<br />
**[[3zg6]] – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn<br />
**[[3zg6]] – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn<br />
-
**[[5mgn]], [[5mfz]], [[5mfp]], [[5mf6]] – hSIRT6 + activator + Zn<br />
+
**[[5mgn]], [[5mfz]], [[5mfp]], [[5mf6]], [[6xv1]], [[6xvg]], [[6zu4]] – hSIRT6 + activator + Zn<br />
-
**[[5y2f]] – 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
 +
 +
**[[1zz0]], [[5g1b]] – AbHDAH – ''Alcalifenaceae bacterium''<br />
 +
**[[1zz3]], [[2gh6]], [[2vcg]], [[5g1a]], [[5g1c]], [[5g3w]] – AbHDAH + inhibitor <br />
 +
**[[5g17]] – AbHDAH (mutant) + inhibitor <br />
 +
**[[1zz1]] – AbHDAH + SAHA <br />
 +
**[[5g0y]] – PaHDAH – ''Pseudomonas aeruginosa''<br />
 +
**[[5li3]] – PaHDAH + inhibitor <br />
}}
}}
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

3D Structures of histone deacetylase

Updated on 22-May-2023

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel

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