8FDV: Lysine-specific histone demethylase 1A

LSD1-CoREST in complex N-formyl FAD and SNAG peptide. Determined by X-ray diffraction at 2.95 Å resolution. Released 12 Jun 2024.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,425
Mol. weight: 113.43 kDa
Ligands: HUF
Released: 12 Jun 2024

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

Secondary structure: helices and β-sheets

8FDV contains 39 α-helices and 38 β-strands across 3 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
α-helix	356-357	2
β-strand	363	1	7
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	408-467	60
α-helix	469	1
α-helix	471	1
α-helix	474-513	40
α-helix	515-517	3
α-helix	525-540	16
β-strand	547	1	10
β-strand	548	1	9
α-helix	554-558	5
α-helix	559-560	2
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	627-631	5
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	13
β-strand	677-679	3	13
β-strand	690-695	6	13
β-strand	702-707	6	13
α-helix	709-715	7
α-helix	720-735	16
β-strand	745-748	4	13
β-strand	762-763	2	12
β-strand	765	1	10
α-helix	770-775	6
β-strand	780	1	2
β-strand	796-798	3	2
α-helix	801-803	3
α-helix	812-829	18

Chain B: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	312	1	14
β-strand	314	1	14
α-helix	318-325	8
α-helix	330-362	33
α-helix	368-370	3
α-helix	385-398	14
α-helix	402-409	8
α-helix	414-424	11
α-helix	430-439	10

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

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)
Zinc finger protein SNAI1	C	protein	9	Homo sapiens	O95863 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8FDV_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

>8FDV_2 REST corepressor 1 (chains B)
GPLGSPEFRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTN
SALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQ
VKNFFVNYRRRFNIDEVLQEWEAE

Sequence of entity 3 (C), FASTA

>8FDV_3 Zinc finger protein SNAI1 (chains C)
PRSFLVRKP

Ligands and cofactors

ID	Name	Formula	Copies
HUF	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxid…	C28 H35 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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