6E1F: Lysine-specific histone demethylase 1A

Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1. Determined by X-ray diffraction at 1.16 Å resolution. Released 10 Jul 2019.

Method: X-ray diffraction
Resolution: 1.16 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,437
Mol. weight: 41.13 kDa
Released: 10 Jul 2019

Explore 6E1F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E1F contains 31 α-helices and 0 β-strands across 4 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.

Chains A and C: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	190-195	6
α-helix	197-200	4
α-helix	204-223	20
α-helix	231-236	6
α-helix	239	1
α-helix	242-244	3
α-helix	246-258	13

Chain B: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	180-182	3
α-helix	190-195	6
α-helix	197-200	4
α-helix	205-223	19
α-helix	231-237	7
α-helix	239	1
α-helix	242-244	3
α-helix	246-258	13
α-helix	263-265	3

Chain D: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	190-195	6
α-helix	197-200	4
α-helix	204-207	4
α-helix	208-223	16
α-helix	231-237	7
α-helix	238-239	2
α-helix	246-258	13
α-helix	263-265	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1A	A, B, C, D	protein	89	Homo sapiens	O60341 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6E1F_1 Lysine-specific histone demethylase 1A (chains A, B, C, D)
GPGSLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQL
EAPYNSDTVLVHRVHSYLERHGLINFGIY

Primary citation

Transient and highly ordered structural domains exist within the N-terminus of LSD1 and differentially interact with mononucleosomes. Zeng, D., Brown, B.P., Luka, Z. et al. To be published.

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

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
6KGQ 2.32 Å, LSD1-FCPA-MPE five-membered ring adduct model

Browse structure collections

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