2UXN: Lysine-specific histone demethylase 1

Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation. Determined by X-ray diffraction at 2.72 Å resolution. Released 29 May 2007.

Method: X-ray diffraction
Resolution: 2.72 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 6,469
Mol. weight: 103.82 kDa
Ligands: FDA
Released: 29 May 2007

Explore 2UXN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2UXN contains 41 α-helices and 34 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 33 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	174-180	7
α-helix	190-195	6
α-helix	197-201	5
α-helix	204-223	20
β-strand	227	1	1
α-helix	231-237	7
α-helix	238-239	2
α-helix	246-258	13
β-strand	268	1	1
α-helix	272-274	3
β-strand	280-284	5	2
α-helix	288-300	13
β-strand	303-307	5	2
β-strand	319-322	4	3
β-strand	325-328	4	3
β-strand	333-334	2	4
β-strand	338	1	5
α-helix	342-348	7
β-strand	353-355	3	4
α-helix	356-357	2
β-strand	362-363	2	6
α-helix	368	1
β-strand	369	1	6
α-helix	370-371	2
α-helix	372-394	23
β-strand	400	1	7
β-strand	405	1	7
α-helix	406	1
β-strand	407	1	8
α-helix	408-467	60
α-helix	469	1
α-helix	474-512	39
α-helix	523-539	17
β-strand	547	1	9
β-strand	548	1	8
α-helix	556-558	3
α-helix	559-560	2
β-strand	561	1	5
β-strand	565-567	3	4
α-helix	573-579	7
β-strand	583-585	3	2
β-strand	588-596	9	10
β-strand	599-606	8	10
β-strand	613-618	6	10
β-strand	620-623	4	2
α-helix	627-631	5
β-strand	638-640	3	10
α-helix	642-644	3
α-helix	645-653	9
β-strand	655-656	2	11
β-strand	660-665	6	6
β-strand	677-680	4	6
β-strand	693-695	3	6
β-strand	702-707	6	6
α-helix	709-715	7
α-helix	720-735	16
α-helix	741-743	3
β-strand	745-748	4	6
β-strand	762-763	2	11
β-strand	765	1	9
α-helix	770-777	8
β-strand	780	1	2
α-helix	782-784	3
α-helix	789-794	6
β-strand	796-798	3	2
α-helix	801-803	3
α-helix	811-829	19

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	310-311	2
α-helix	318-324	7
α-helix	330-362	33
α-helix	368-370	3
α-helix	385-398	14
α-helix	402-409	8
α-helix	414-423	10
α-helix	430-438	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1	A	protein	666	HOMO SAPIENS	O60341 (AlphaFold model)
Rest corepressor 1	B	protein	235	HOMO SAPIENS	Q9UKL0 (AlphaFold model)
Histone H3.1	E	protein	21	HOMO SAPIENS	P68431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2UXN_1 LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 (chains A)
PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLT
FEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSG
LAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVN
MELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQ
ALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKP
PRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILD
WHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAV
RQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSA
VQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGE
AAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSG
NDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFL
GAMYTL

Sequence of entity 2 (B), FASTA

>2UXN_2 REST COREPRESSOR 1 (chains B)
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFGRPTETVPQVKKEKHSTQAKNRAK
RKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGI
EPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRR
FNIDEVLQEWEAEHGKEETNGPSNQKPVKSPDNSIKMPEEEDEAPVLDVRYASAS

Sequence of entity 3 (E), FASTA

>2UXN_3 HISTONE H3.1 (chains E)
ARTXQTARKSTGGKAPRKQLA

Ligands and cofactors

ID	Name	Formula	Copies
FDA	Dihydroflavine-adenine dinucleotide	C27 H35 N9 O15 P2	1

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Structural Basis of Histone Demethylation by Lsd1 Revealed by Suicide Inactivation. Yang, M., Culhane, J.C., Szewczuk, L.M. et al. Nat Struct Mol Biol (2007) 14:535. DOI 10.1038/NSMB1255 · PubMed

Other PDB entries of the same protein (UniProt O60341 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6E1F 1.16 Å, Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1
5IT3 1.4 Å, Swirm domain of human Lsd1
5AFW 1.6 Å, Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation
7JK7 1.96 Å, Crystal structure of Importin alpha 2 in complex with LSD1 NLS S111E mutant
7JJM 2.06 Å, Crystal structure of Importin alpha 2 in complex with LSD1 NLS
2Z3Y 2.25 Å, Crystal structure of Lysine-specific demethylase1
2Z5U 2.25 Å, Crystal structure of Lysine-specific histone demethylase 1
6KGO 2.25 Å, LSD1-S2157 five-membered ring adduct model
6KGP 2.25 Å, LSD1-S2157 N5 adduct model
7E0G 2.25 Å, Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct
7XW8 2.28 Å, Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418 distomer,…
2DW4 2.3 Å, Crystal structure of human LSD1 at 2.3 A resolution

Browse structure collections

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