5L3D: Human LSD1/CoREST: LSD1 Y761H mutation

Human LSD1/CoREST: LSD1 Y761H mutation. Determined by X-ray diffraction at 2.6 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,408
Mol. weight: 146.87 kDa
Ligands: FAD
Released: 4 May 2016

Explore 5L3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L3D contains 40 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: 32 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	174-180	7
α-helix	190-195	6
α-helix	197-201	5
α-helix	204-223	20
β-strand	227	1	1
α-helix	231-236	6
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	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	362-363	2	7
α-helix	368	1
β-strand	369	1	7
α-helix	370-371	2
α-helix	372-394	23
β-strand	400	1	8
β-strand	405	1	8
α-helix	406	1
β-strand	407	1	9
α-helix	408-467	60
α-helix	469	1
α-helix	474-513	40
α-helix	523-539	17
β-strand	547	1	10
β-strand	548	1	9
α-helix	556-558	3
α-helix	559-560	2
β-strand	561	1	6
β-strand	565-567	3	5
α-helix	573-578	6
β-strand	584-585	2	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	677-680	4	7
β-strand	693-695	3	7
β-strand	702-707	6	7
α-helix	709-715	7
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	771-777	7
β-strand	780	1	2
α-helix	782-784	3
β-strand	796-798	3	2
α-helix	801-803	3
α-helix	811-829	19
α-helix	833-835	3

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	310-311	2
α-helix	318-324	7
α-helix	330-362	33
α-helix	373-375	3
α-helix	385-398	14
α-helix	402-409	8
α-helix	414-423	10
α-helix	430-439	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1A	A	protein	852	Homo sapiens	O60341 (AlphaFold model)
REST corepressor 1	B	protein	482	Homo sapiens	Q9UKL0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5L3D_1 Lysine-specific histone demethylase 1A (chains A)
MLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTP
RKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEY
REMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGVEGAAFQ
SRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEA
PYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSF
GMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKC
PLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLV
KSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFAN
ATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGC
EVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLN
KVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISD
DVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSHSYVAAGSSGNDYDLMAQPI
TPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQA
TPGVPAQQSPSM

Sequence of entity 2 (B), FASTA

>5L3D_2 REST corepressor 1 (chains B)
MVEKGPEVSGKRRGRNNAAASASAAAASAAASAACASPAATAASGAAASSASAAAASAAA
APNNGQNKSLAAAAPNGNSSSNSWEEGSSGSSSDEEHGGGGMRVGPQYQAVVPDFDPAKL
ARRSQERDNLGMLVWSPNQNLSEAKLDEYIAIAKEKHGYNMEQALGMLFWHKHNIEKSLA
DLPNFTPFPDEWTVEDKVLFEQAFSFHGKTFHRIQQMLPDKSIASLVKFYYSWKKTRTKT
SVMDRHARKQKREREESEDELEEANGNNPIDIEVDQNKESKKEVPPTETVPQVKKEKHST
QAKNRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALK
EKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNF
FVNYRRRFNIDEVLQEWEAEHGKEETNGPSNQKPVKSPDNSIKMPEEEDEAPVLDVRYAS
AS

Ligands and cofactors

ID	Name	Formula	Copies
FAD	Flavin-adenine dinucleotide	C27 H33 N9 O15 P2	1

Primary citation

LSD1/KDM1A mutations associated to a newly described form of intellectual disability impair demethylase activity and binding to transcription factors. Pilotto, S., Speranzini, V., Marabelli, C. et al. Hum Mol Genet (2016) 25:2578-2587. DOI 10.1093/hmg/ddw120 · 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 5L3D 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.