6KGL: LSD1-CoREST-S2101 N5 adduct model

LSD1-CoREST-S2101 N5 adduct model. Determined by X-ray diffraction at 2.7 Å resolution. Released 25 Mar 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,383
Mol. weight: 91.52 kDa
Ligands: FAD, DJ0
Released: 25 Mar 2020

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

Secondary structure: helices and β-sheets

6KGL contains 42 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: 33 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	173-180	8
α-helix	190-195	6
α-helix	197-200	4
α-helix	204-222	19
β-strand	227	1	1
α-helix	231-237	7
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	319-322	4	4
β-strand	325-328	4	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	362-364	3	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	474-511	38
α-helix	515-517	3
α-helix	523-540	18
α-helix	544-546	3
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	573-579	7
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	7
β-strand	677-681	5	7
β-strand	690-696	7	7
β-strand	702-707	6	7
α-helix	710-715	6
α-helix	720-735	16
α-helix	741-743	3
β-strand	745-748	4	7
β-strand	762-763	2	12
β-strand	765	1	10
α-helix	770-777	8
α-helix	779	1
β-strand	780	1	2
α-helix	782-784	3
α-helix	789-794	6
β-strand	796-798	3	2
α-helix	801-803	3
α-helix	811-829	19

Chain B: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	310-311	2
α-helix	318-325	8
α-helix	330-362	33
α-helix	368-370	3
α-helix	371-373	3
α-helix	385-398	14
α-helix	402-409	8
α-helix	414-423	10
α-helix	430-437	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1A	A	protein	669	Homo sapiens	O60341 (AlphaFold model)
REST corepressor 1	B	protein	140	Homo sapiens	Q9UKL0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6KGL_1 Lysine-specific histone demethylase 1A (chains A)
GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDN
PKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIII
GSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAV
VSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNK
PVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKE
ASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSR
DRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDI
KLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLP
EWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILL
ALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYV
AAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGR
IADQFLGAM

Sequence of entity 2 (B), FASTA

>6KGL_2 REST corepressor 1 (chains B)
GSSGSASRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALK
EKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNF
FVNYRRRFNIDEVLQEWEAE

Ligands and cofactors

ID	Name	Formula	Copies
FAD	Flavin-adenine dinucleotide	C27 H33 N9 O15 P2	1
DJ0	3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal	C16 H14 F2 O2	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Niwa, H., Sato, S., Handa, N. et al. ChemMedChem (2020) 15:787-793. DOI 10.1002/cmdc.202000014 · 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

About this viewer

MolViewer shows 6KGL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.