Lysine-specific histone demethylase 3D structures

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*lysine-specific histone demethylase 1A
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*LSD1 or lysine-specific histone demethylase 1A; Domains – SWIRM 174-273; FAD-binding 275-833
-
**[[2com]], [[2l3d]] - hLSD1 SWIRM domain 174-273 – human – NMR<br />
+
**[[2com]], [[2l3d]] - hLSD1 SWIRM domain – human – NMR
**[[5it3]], [[6e1f]] - hLSD1 SWIRM domain<br />
**[[5it3]], [[6e1f]] - hLSD1 SWIRM domain<br />
-
**[[2h94]], [[2dw4]], [[2z3y]], [[2z5u]], [[4fwe]], [[4fwj]], [[4gu1]] – hLSD1 170-833<br />
+
**[[2h94]], [[2dw4]], [[2z3y]], [[2z5u]], [[6nqm]] – hLSD1 SWIRM+FAD-binding domains
-
**[[2hko]] – hLSD1 (mutant)<br />
+
**[[2hko]] – hLSD1 SWIRM+FAD-binding domains (mutant)
-
**[[2ejr]], [[3abt]], [[3abu]] – hLSD1 + tranylcypromine derivative<br />
+
**[[2ejr]], [[3abt]], [[3abu]] – hLSD1 SWIRM+FAD-binding domains + tranylcypromine derivative
-
**[[4gut]], [[4guu]] – hLSD1 + oxidoreductase<br />
+
**[[6nqu]], [[6kgo]], [[6kgp]], [[6kgq]], [[6kgr]], [[7vqs]], [[7vqt]], [[7vqu]], [[7w3l]], [[8inl]] – hLSD1 SWIRM+FAD-binding domains + inhibitor<br />
-
**[[6nqu]], [[6kgo]], [[6kgp]], [[6kgq]], [[6kgr]] – hLSD1 + inhibitor<br />
+
**[[6nr5]] – hLSD1 SWIRM+FAD-binding domains + phenelzine sulfate<br />
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**[[6nr5]] – hLSD1 + phenelzine sulfate<br />
+
**[[7xw8]] – hLSD1 SWIRM+FAD-binding domains + pteridine derivative<br />
-
 
+
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*LSD1 complex with histone H3 peptide
+
-
 
+
-
**[[4fwf]] – hLSD1 + histone 3.1 peptide<br />
+
*LSD1 complex with CoREST
*LSD1 complex with CoREST
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**[[2iw5]], [[2uxn]], [[2uxx]] - hLSD1 SWIRM + amine oxidase domains + CoREST SANT1 and SANT2 domains<br />
+
**[[4czz]] - hLSD1 + CoREST <br />
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**[[2v1d]], [[5x60]], [[5h6r]], [[5h6q]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + histone H3 residues 2-22 (mutant)<br />
+
**[[5l3b]], [[5l3c]], [[5l3d]] - hLSD1 (mutant) + CoREST <br />
-
**[[2x0l]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + histone H3 residues 1-16<br />
+
**[[7zry]] – hLSD1 + CoREST SANT1 and SANT2 domains 305-482<br />
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**[[2xaf]], [[2xag]], [[2xah]], [[2xaj]], [[2xaq]], [[2xas]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + tranylcypromine derivative<br />
+
**[[4bay]], [[4kum]] - hLSD1 SWIRM + FAD domains + CoREST residues 289-485 <br />
-
**[[2y48]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + zinc finger protein SNAIL N terminal<br />
+
**[[2iw5]], [[6kgk]] - hLSD1 SWIRM+FAD-binding domains + CoREST <br />
-
**[[3zms]], [[3zmt]], [[3zmu]], [[3zmv]], [[3zmz]], [[3zn0]], [[3zn1]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + zinc finger protein IA-1 peptide <br />
+
**[[2xaf]], [[2xag]], [[2xah]], [[2xaj]], [[2xaq]], [[2xas]] - hLSD1 SWIRM+FAD-binding domains + CoREST SANT1 and SANT2 domains + tranylcypromine derivative
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**[[4bay]] - hLSD1 residues 192-876 + CoREST residues 308-440 <br />
+
-
**[[4kum]] - hLSD1 SWIRM + FAD domains + CoREST residues 289-485 <br />
+
-
**[[4czz]], [[6kgk]] - hLSD1 + CoREST <br />
+
-
**[[5l3b]], [[5l3c]], [[5l3d]], - hLSD1 (mutant) + CoREST <br />
+
**[[4uv8]], [[4uv9]], [[4uva]], [[4uvb]], [[4uvc]] - hLSD1 + CoREST + irreversible inhibitor<br />
**[[4uv8]], [[4uv9]], [[4uva]], [[4uvb]], [[4uvc]] - hLSD1 + CoREST + irreversible inhibitor<br />
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**[[5l3e]], [[5lbq]], [[5lgn]], [[5lgt]], [[5lgu]], [[5lhg]], [[5lhh]], [[5lhi]] - hLSD1 + CoREST + reversible inhibitor<br />
+
**[[4uxn]], [[6te1]], [[6tuy]], [[8bop]], [[8f2z]], [[8f30]], [[8f6s]], [[8fj4]], [[8fq6]], [[8fri]], [[8frq]], [[8frv]], [[8fsk]], [[8gj6]], [[8ul6]], [[8ul8]], [[8ulb]], [[8ulc]], [[8umq]], [[9el7]], [[9el8]], [[9ela]], [[9f0a]] - hLSD1 + CoREST 308-443 + inhibitor<br />
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**[[5l3f]], [[5l3g]] - hLSD1 + CoREST + polmyxin peptide<br />
+
**[[5yjb]], [[6k3e]], [[6kgl]], [[6kgm]], [[6kgn]], [[6w4k]], [[7e0g]] - hLSD1 SWIRM+FAD-binding domains + CoREST 311-443 + inhibitor<br />
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**[[4xbf]] - hLSD1 + CoREST + RNA<br />
+
**[[9fwg]] - hLSD1 + CoREST + drug<br />
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**[[4uxn]], [[5yjb]], [[6k3e]], [[6kgl]], [[6kgm]], [[6kgn]], [[6te1]] - hLSD1 + CoREST + pyrrolydine inhibitor<br />
+
**[[8jf5]], [[8ym7]], [[9dbp]] - hLSD1 SWIRM+FAD-binding domains + CoREST + FAD + inhibitor<br />
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**[[6s35]] - hLSD1 + CoREST + peptide inhibitor<br />
+
 
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**[[6vyp]] - hLSD1 + CoREST + histones + DNA<br />
+
*LSD1 complex with CoREST and protein
 +
 
 +
*[[2v1d]], [[5x60]], [[5h6r]], [[5h6q]] - hLSD1 SWIRM+FAD-binding domains + CoREST SANT1 and SANT2 domains + histone H3 residues 2-22 (mutant)
 +
*[[2x0l]] - hLSD1 SWIRM+FAD-binding domains + CoREST SANT1 and SANT2 domains + histone H3 residues 1-16
 +
**[[2y48]] - hLSD1 SWIRM+FAD-binding domains + CoREST SANT1 and SANT2 domains + zinc finger protein SNAIL N terminal<br />
 +
**[[3zms]], [[3zmt]], [[3zmu]], [[3zmv]], [[3zmz]], [[3zn0]], [[3zn1]] - hLSD1 SWIRM+FAD-binding domains + CoREST SANT1 and SANT2 domains + zinc finger protein IA-1 peptide <br />
 +
**[[6s35]], [[6wc6]], [[7cdc]], [[7cdd]], [[7cde]], [[7cdf]], [[7cdg]] - hLSD1 SWIRM+FAD-binding domains + CoREST + FAD + peptide inhibitor<br />
 +
**[[6wc6]] - hLSD1 SWIRM+FAD-binding domains + CoREST + LSD1 peptide <br />
 +
**[[8uni]] - hLSD1 + CoREST + H3 peptide + inhibitor<br />
 +
**[[8q1g]], [[8q1j]], [[8uom]] - hLSD1 SWIRM+FAD-binding domains + CoREST + H3 peptide + FAD<br />
 +
**[[8q1d]] - hLSD1 SWIRM+FAD-binding domains (mutant) + CoREST + H3 peptide + FAD<br />
 +
**[[2uxn]], [[2uxx]] - hLSD1 SWIRM+FAD-binding domains + CoREST + H3 peptide + FDA<br />
 +
**[[8box]], [[8f59]], [[8fdv]] - hLSD1 + CoREST + FAD + SNAG peptide <br />
 +
**[[8fj7]], [[8ulz]] - hLSD1 + CoREST + inhibitor + SNAG peptide <br />
 +
**[[6vyp]] - hLSD1 SWIRM+FAD-binding domains + CoREST + nucleosome + DNA<br />
 +
**[[9dwu]] - hLSD1 SWIRM+FAD-binding domains + CoREST 311-379 + U2AF2 – Cryo EM<br />
 +
 
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*lysine-specific histone demethylase 1B
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*LSD2 or lysine-specific histone demethylase 1B
**[[4gu1]] – hLSD2<br />
**[[4gu1]] – hLSD2<br />
 +
**[[4fwe]], [[4fwj]], [[4gu1]] – hLSD2 + FAD<br />
**[[4gur]], [[4gus]], [[4hsu]] – hLSD2 + NPAC + histone 3.3 peptide <br />
**[[4gur]], [[4gus]], [[4hsu]] – hLSD2 + NPAC + histone 3.3 peptide <br />
**[[4gut]] – hLSD2 + NPAC <br />
**[[4gut]] – hLSD2 + NPAC <br />
**[[4guu]] – hLSD2 + NPAC + tranylcypromine <br />
**[[4guu]] – hLSD2 + NPAC + tranylcypromine <br />
**[[4gu0]] – hLSD2 + histone 3.3 peptide <br />
**[[4gu0]] – hLSD2 + histone 3.3 peptide <br />
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**[[6r25]], [[6r1u]] – hLSD2 + NPAC + histones 3,4,2A,2B + DNA – Cryo EM <br />
+
**[[4fwf]] – hLSD2 + histone 3.1 peptide + FAD<br />
 +
**[[7xe1]], [[7xe2]], [[7xe3]] – hLSD2 + inhibitor <br />
 +
**[[6r25]], [[6r1t]], [[6r1u]] – hLSD2 + NPAC + histones 3,4,2A,2B + DNA – Cryo EM <br />
 +
**[[4gut]], [[4guu]] – hLSD2 51-822 + oxidoreductase<br />
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*lysine-specific histone demethylase 5A or JARID1A or KDM5A. Domains: Jmj 1-87 + 348-588
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*lysine-specific histone demethylase 5A or JARID1A or KDM5A. Domains: Jmj 1-87 + 348-588, ARID 85-175; PHD1 287-344; PHD 1609-1659
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**[[6dq4]], [[6dq5]], [[6dq6]], [[6dq7]], [[6dq8]], [[6dq9]], [[6dqa]], [[6dqb]], [[6dqc]], [[6dqd]], [[6dqe]], [[6dqf]] – hLSD5A jmj domain + inhibitor<br />
+
**[[5e6h]] – hLSD5A jmj domain <br />
 +
**[[5isl]], [[5ivb]], [[5ivc]], [[5ive]], [[5ivf]], [[5ivj]], [[5ivv]], [[5ivy]], [[5iw0]], [[5iwf]], [[5k4l]], [[5v9p]], [[5v9t]], [[6bgu]], [[6bgv]], [[6bgw]], [[6bgx]], [[6bgy]], [[6bgz]], [[6bh0]], [[6bh1]], [[6bh2]], [[6bh3]], [[6bh4]], [[6bh5]],[[6dq4]], [[6dq5]], [[6dq6]], [[6dq7]], [[6dq8]], [[6dq9]], [[6dqa]], [[6dqb]], [[6dqc]], [[6dqd]], [[6dqe]], [[6dqf]] – hLSD5A jmj domain + inhibitor<br />
 +
**[[2kgg]], [[7klo]] – hLSD5A PHD domain - NMR<br />
 +
**[[7klo]] – hLSD5A PHD1 domain - NMR<br />
 +
**[[7klr]] – hLSD5A PHD1 domain + H3 peptide<br />
 +
**[[3gl6]] – hLSD5A PHD domain + H3 peptide<br />
 +
**[[5c11]] – hLSD5A PHD domain + H3 peptide <br />
 +
**[[2kgi]] – hLSD5A PHD domain + H3 peptide - NMR<br />
 +
**[[2jxj]] – hLSD5A ARID domain - NMR<br />
*lysine-specific histone demethylase 5B or JARID1B or KDM5B. Domains: zinc finger 1 306-360; PHD-type zinc finger 1487-1544; ARID 94-208; JmjC 26-101 + 374-772
*lysine-specific histone demethylase 5B or JARID1B or KDM5B. Domains: zinc finger 1 306-360; PHD-type zinc finger 1487-1544; ARID 94-208; JmjC 26-101 + 374-772
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**[[6g8f]], [[6fuk]], [[6ful]], [[6ete]] – hKDM6A + inhibitor<br />
**[[6g8f]], [[6fuk]], [[6ful]], [[6ete]] – hKDM6A + inhibitor<br />
 +
**[[3avr]], [[3avs]] – hKDM6A 880-1401 + H3 peptide + oxalylglycine<br />
*lysine-specific histone demethylase Ref6 see [[Jumonji domain-containing protein 3D structures]]
*lysine-specific histone demethylase Ref6 see [[Jumonji domain-containing protein 3D structures]]

Current revision

3D structures of lysine-specific histone demethylase

Updated on 29-October-2025


Proteopedia Page Contributors and Editors (what is this?)

Michal Harel

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