7XE3: LSD2

Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024). Determined by X-ray diffraction at 2.82 Å resolution. Released 14 Sept 2022.

Method: X-ray diffraction
Resolution: 2.82 Å
Organism: Homo sapiens
Chains: 2
Atoms: 12,142
Mol. weight: 181 kDa
Ligands: ZN, FAD, 8A2, FLC
Released: 14 Sept 2022

Explore 7XE3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XE3 contains 89 α-helices and 82 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: 46 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	1
β-strand	65	1	2
β-strand	79	1	1
β-strand	82-86	5	2
β-strand	89-92	4	2
α-helix	93-100	8
α-helix	107-120	14
α-helix	124-125	2
α-helix	127-134	8
α-helix	137-138	2
β-strand	139-141	3	3
β-strand	150-152	3	3
α-helix	153-154	2
α-helix	157-160	4
α-helix	161-166	6
α-helix	184-186	3
α-helix	188-189	2
α-helix	191-196	6
α-helix	199-203	5
β-strand	211	1	4
α-helix	217-219	3
α-helix	225-228	4
β-strand	230	1	4
β-strand	272	1	5
α-helix	273-274	2
α-helix	283	1
β-strand	284	1	5
α-helix	285	1
α-helix	291-296	6
α-helix	298-300	3
α-helix	305-320	16
α-helix	328-331	4
α-helix	332-334	3
α-helix	341-358	18
α-helix	378-381	4
β-strand	384-388	5	6
α-helix	392-404	13
β-strand	407-411	5	6
β-strand	423-424	2	7
β-strand	432-433	2	7
β-strand	438-440	3	8
α-helix	446-454	9
β-strand	459-460	2	8
α-helix	461-462	2
β-strand	467-469	3	9
α-helix	473	1
β-strand	474	1	9
α-helix	475-476	2
α-helix	477-498	22
α-helix	503-505	3
β-strand	508	1	10
α-helix	509-524	16
α-helix	530-547	18
β-strand	554	1	11
β-strand	555	1	10
α-helix	561-564	4
β-strand	572-574	3	8
α-helix	579-587	9
β-strand	591-593	3	6
β-strand	598-602	5	12
β-strand	608-612	5	12
β-strand	617-620	4	12
β-strand	622-625	4	6
α-helix	629-633	5
β-strand	638-640	3	12
α-helix	642-644	3
α-helix	645-653	9
β-strand	654-657	4	13
β-strand	659-665	7	9
α-helix	672-675	4
β-strand	680-684	5	9
β-strand	693-699	7	9
β-strand	708-714	7	9
α-helix	716-720	5
α-helix	726-740	15
α-helix	747-749	3
β-strand	751-754	4	9
α-helix	757-759	3
β-strand	767-770	4	13
β-strand	771	1	11
α-helix	777-783	7
β-strand	786	1	6
β-strand	790-792	3	6
α-helix	795-797	3
α-helix	805-821	17

Chain B: 43 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	14
β-strand	65	1	15
β-strand	79	1	14
β-strand	82-86	5	15
β-strand	89-92	4	15
α-helix	93-100	8
α-helix	107-119	13
α-helix	124-125	2
α-helix	127-134	8
α-helix	137-138	2
β-strand	139-141	3	16
β-strand	150-152	3	16
α-helix	157-159	3
α-helix	161-165	5
α-helix	188-190	3
α-helix	192-195	4
α-helix	199-203	5
β-strand	211	1	17
β-strand	212	1	18
α-helix	217-220	4
α-helix	225-228	4
β-strand	230	1	17
β-strand	272	1	19
α-helix	277-279	3
β-strand	280	1	20
β-strand	284	1	19
α-helix	291-296	6
α-helix	298-300	3
α-helix	305-320	16
α-helix	328-331	4
α-helix	332-334	3
β-strand	336	1	18
α-helix	341-359	19
α-helix	378-381	4
β-strand	384-388	5	21
α-helix	392-404	13
β-strand	407-411	5	21
β-strand	423-424	2	22
β-strand	432-433	2	22
β-strand	438-440	3	23
α-helix	446-454	9
β-strand	459-460	2	23
β-strand	467-469	3	24
α-helix	473	1
β-strand	474	1	24
α-helix	475-476	2
α-helix	477-497	21
α-helix	498-500	3
α-helix	503-505	3
β-strand	508	1	25
α-helix	509-524	16
α-helix	530-547	18
β-strand	554	1	26
β-strand	555	1	25
α-helix	561-564	4
α-helix	566	1
β-strand	567	1	20
β-strand	572-574	3	23
α-helix	580-586	7
β-strand	592-593	2	21
β-strand	598-603	6	27
β-strand	608-612	5	27
β-strand	617-620	4	27
β-strand	622-625	4	21
α-helix	629-633	5
β-strand	638-640	3	27
α-helix	642-644	3
α-helix	645-653	9
β-strand	654-657	4	28
β-strand	659-665	7	24
α-helix	672-675	4
β-strand	680-684	5	24
β-strand	693-699	7	24
β-strand	708-714	7	24
α-helix	717-721	5
α-helix	726-740	15
α-helix	747-749	3
β-strand	751-754	4	24
α-helix	757-759	3
β-strand	767-770	4	28
β-strand	771	1	26
α-helix	777-783	7
β-strand	786	1	21
β-strand	790-792	3	21
α-helix	795-797	3
α-helix	805-820	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1B	A, B	protein	793	Homo sapiens	Q8NB78 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7XE3_1 Lysine-specific histone demethylase 1B (chains A, B)
AKKKATETTDEDEDGGSEKKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGE
HFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRK
WRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPP
LLKDSVAAPLLSAYYPDCVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYF
QPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQ
KCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIG
AGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVAL
MCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPL
GEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFA
GDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPL
ALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSAS
KRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDP
TKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAY
LSGVREASKIAAF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
FAD	Flavin-adenine dinucleotide	C27 H33 N9 O15 P2	2
8A2	3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal	C9 H7 Br F2 O	2
FLC	Citrate anion	C6 H5 O7	1

Water and common crystallization additives (PG4, EDO) are not listed.

Primary citation

Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2. Niwa, H., Watanabe, C., Sato, S. et al. ACS Med Chem Lett (2022) 13:1485-1492. DOI 10.1021/acsmedchemlett.2c00294

Other PDB entries of the same protein (UniProt Q8NB78 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HSU 1.99 Å, Crystal structure of LSD2-NPAC with H3(1-26)in space group P21
4GUT 2.0 Å, Crystal structure of LSD2-NPAC
7XE2 2.05 Å, Crystal structure of LSD2 in complex with trans-4-Br-PCPA
7XE1 2.07 Å, Crystal structure of LSD2 in complex with cis-4-Br-PCPA
4FWE 2.13 Å, Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A
4GUS 2.23 Å, Crystal structure of LSD2-NPAC with H3 in space group P3221
4GUU 2.3 Å, Crystal structure of LSD2-NPAC with tranylcypromine
4GUR 2.51 Å, Crystal structure of LSD2-NPAC with H3 in space group P21
4FWF 2.7 Å, Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic
4FWJ 2.9 Å, Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A
4GU1 2.94 Å, Crystal structure of LSD2
4GU0 3.1 Å, Crystal structure of LSD2 with H3

Browse structure collections

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