5IT3: Swirm domain of human Lsd1

Swirm domain of human Lsd1. Determined by X-ray diffraction at 1.4 Å resolution. Released 18 May 2016.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,646
Mol. weight: 19.92 kDa
Ligands: MG
Released: 18 May 2016

Explore 5IT3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IT3 contains 12 α-helices and 0 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: 6 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	246-258	13

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	190-195	6
α-helix	197-200	4
α-helix	204-223	20
α-helix	231-235	5
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	protein	85	Homo sapiens	O60341 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IT3_1 Lysine-specific histone demethylase 1A (chains A, B)
LPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPY
NSDTVLVHRVHSYLERHGLINFGIY

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Primary citation

A Tlx-interacting peptide of Lsd1 inhibits the proliferation of brain tumor stem cells. Hu, R., Sun, X., Hameed, U.F.S. 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:

6E1F 1.16 Å, Crystal structure of the SWIRM domain of human histone lysine-specific demethylase 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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