8ULZ: LSD1-CoREST

LSD1-CoREST in complex with T18 and SNAG peptide. Determined by X-ray diffraction at 3.32 Å resolution. Released 27 Aug 2025.

Method: X-ray diffraction
Resolution: 3.32 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,400
Mol. weight: 113.65 kDa
Ligands: YAO
Released: 27 Aug 2025

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

Secondary structure: helices and β-sheets

8ULZ contains 39 α-helices and 36 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, 36 β-strands

Element	Residues	Length	Sheet
α-helix	174-180	7
α-helix	190-195	6
α-helix	197-200	4
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
β-strand	287	1	3
α-helix	288-299	12
β-strand	303-307	5	2
β-strand	314	1	3
β-strand	320-322	3	4
β-strand	325-327	3	4
β-strand	333-334	2	5
β-strand	338	1	6
α-helix	341-348	8
β-strand	353-355	3	5
β-strand	362-363	2	7
α-helix	368	1
β-strand	369	1	7
α-helix	370-371	2
α-helix	372-394	23
β-strand	400-401	2	8
β-strand	404-405	2	8
α-helix	406	1
β-strand	407	1	9
α-helix	408-466	59
α-helix	469	1
α-helix	474-512	39
α-helix	523-539	17
β-strand	547	1	10
β-strand	548	1	9
α-helix	554-558	5
β-strand	561	1	6
β-strand	565-567	3	5
α-helix	573-578	6
β-strand	583-585	3	2
β-strand	588-596	9	11
β-strand	599-606	8	11
β-strand	613-618	6	11
β-strand	620-623	4	2
α-helix	627-630	4
β-strand	638-640	3	11
α-helix	642-644	3
α-helix	645-653	9
β-strand	655-656	2	12
β-strand	660-665	6	7
β-strand	677-680	4	7
β-strand	693-696	4	7
β-strand	702-707	6	7
α-helix	709-715	7
α-helix	720-735	16
α-helix	741-743	3
β-strand	746-748	3	7
β-strand	762-763	2	12
β-strand	765	1	10
α-helix	771-775	5
β-strand	780	1	2
α-helix	781-784	4
α-helix	790-791	2
β-strand	796-798	3	2
α-helix	811-826	16
α-helix	827-831	5

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	318-325	8
α-helix	330-334	5
α-helix	337-362	26
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
Zinc finger protein SNAI1	C	protein	9	Homo sapiens	O95863 (AlphaFold model)
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 (C), FASTA

>8ULZ_1 Zinc finger protein SNAI1 (chains C)
PRSFLVRKP

Sequence of entity 2 (A), FASTA

>8ULZ_2 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 3 (B), FASTA

>8ULZ_3 REST corepressor 1 (chains B)
GPLGSPEFRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTN
SALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQ
VKNFFVNYRRRFNIDEVLQEWEAE

Ligands and cofactors

ID	Name	Formula	Copies
YAO	[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl…	C43 H48 N10 O17 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 O95863 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QLI 1.45 Å, A novel phospho-switch in the linker region of the snail zinc finger protein which…
3W5K 2.6 Å, Crystal structure of Snail1 and importin beta complex
8F59 2.8 Å, LSD1-CoREST in complex with AW2 and SNAG peptide
8FJ7 2.8 Å, LSD1-CoREST in complex with T108 and SNAG peptide
8BOX 2.82 Å, LSD1-CoREST in complex with AW4 and SNAG peptide
8FDV 2.95 Å, LSD1-CoREST in complex N-formyl FAD and SNAG peptide
2Y48 3.0 Å, Crystal structure of LSD1-CoREST in complex with a N-terminal SNAIL peptide

Browse structure collections

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