8BOP: LSD1-CoREST

LSD1-CoREST in complex with AW4, long soaking. Determined by X-ray diffraction at 2.74 Å resolution. Released 5 Jun 2024.

Method: X-ray diffraction
Resolution: 2.74 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,368
Mol. weight: 112.58 kDa
Ligands: SV9
Released: 5 Jun 2024

Explore 8BOP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BOP contains 38 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: 31 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	174-179	6
α-helix	190-195	6
α-helix	197-200	4
α-helix	204-223	20
β-strand	227	1	1
α-helix	231-236	6
α-helix	242-244	3
α-helix	246-258	13
β-strand	268	1	1
α-helix	272-274	3
β-strand	280-284	5	2
α-helix	288-299	12
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	341-348	8
β-strand	353-355	3	4
α-helix	356-357	2
β-strand	362-363	2	6
β-strand	369	1	6
α-helix	370-371	2
α-helix	372-394	23
β-strand	400-401	2	7
β-strand	404-405	2	7
α-helix	406	1
β-strand	407	1	8
α-helix	408-465	58
α-helix	474-513	40
α-helix	525-539	15
β-strand	547	1	9
β-strand	548	1	8
α-helix	554-558	5
α-helix	559-560	2
β-strand	561	1	5
β-strand	565-567	3	4
α-helix	571-573	3
α-helix	575-578	4
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	690-695	6	6
β-strand	702-707	6	6
α-helix	709-714	6
α-helix	715-717	3
α-helix	720-735	16
β-strand	745-748	4	6
β-strand	762-763	2	11
β-strand	765	1	9
α-helix	772-775	4
β-strand	780	1	2
α-helix	782-784	3
β-strand	796-798	3	2
α-helix	801-803	3
α-helix	811-830	20

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	310-311	2
α-helix	318-325	8
α-helix	330-362	33
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 1A	A	protein	871	Homo sapiens	O60341 (AlphaFold model)
REST corepressor 1	B	protein	144	Homo sapiens	Q9UKL0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8BOP_1 Lysine-specific histone demethylase 1A (chains A)
GSSHHHHHHSSGLVPRGSHMLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQP
AGLSGPAEVGPGAVGERTPRKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGI
AETPEGRRTSRRKRAKVEYREMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPE
EENESEPEEPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLW
LDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKV
IIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNP
MAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVL
NNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQ
YKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYL
SSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEG
LDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVP
PLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAP
ILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSY
SYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLRE
AGRIADQFLGAMYTLPRQATPGVPAQQSPSM

Sequence of entity 2 (B), FASTA

>8BOP_2 REST corepressor 1 (chains B)
GPLGSPEFRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTN
SALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQ
VKNFFVNYRRRFNIDEVLQEWEAE

Ligands and cofactors

ID	Name	Formula	Copies
SV9	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]…	C48 H51 N9 O16 P2	1

Primary citation

Covalent adduct Grob fragmentation underlies LSD1 demethylase-specific inhibitor mechanism of action and resistance. Waterbury, A.L., Caroli, J., Zhang, O. et al. Nat Commun (2025) 16:3156-3156. DOI 10.1038/s41467-025-57477-3 · 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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