4FWJ: Lysine-specific histone demethylase 1B

Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A. Determined by X-ray diffraction at 2.9 Å resolution. Released 16 Jan 2013.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 12,080
Mol. weight: 180.78 kDa
Ligands: ZN, FAD, PO4
Released: 16 Jan 2013

Explore 4FWJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4FWJ contains 94 α-helices and 78 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: 49 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	1
β-strand	65	1	2
β-strand	79	1	1
β-strand	83-84	2	2
β-strand	90-91	2	2
α-helix	93-95	3
α-helix	104-106	3
α-helix	107-120	14
α-helix	124-125	2
α-helix	127-130	4
α-helix	131-135	5
α-helix	137-138	2
β-strand	139-141	3	3
β-strand	150-152	3	3
α-helix	153-154	2
α-helix	157-159	3
α-helix	161-166	6
α-helix	184-186	3
α-helix	188-189	2
α-helix	192-195	4
α-helix	199-203	5
β-strand	211	1	4
β-strand	212	1	5
α-helix	217-220	4
α-helix	225-228	4
β-strand	230	1	4
β-strand	272	1	6
α-helix	273-274	2
β-strand	284	1	6
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	5
α-helix	342-358	17
β-strand	384-388	5	7
α-helix	392-404	13
β-strand	407-411	5	7
β-strand	423-424	2	8
β-strand	432-433	2	8
β-strand	438-440	3	9
α-helix	446-454	9
β-strand	459-460	2	9
α-helix	461-462	2
β-strand	467-468	2	10
α-helix	469	1
α-helix	473	1
β-strand	474	1	10
α-helix	475-476	2
α-helix	477-497	21
α-helix	498-500	3
α-helix	503-505	3
β-strand	508	1	11
α-helix	509-524	16
α-helix	530-547	18
α-helix	551-553	3
β-strand	554	1	12
β-strand	555	1	11
α-helix	561-564	4
β-strand	572-574	3	9
α-helix	579-587	9
β-strand	592-593	2	7
β-strand	598-602	5	13
β-strand	608-612	5	13
β-strand	617-620	4	13
β-strand	622-625	4	7
α-helix	629-633	5
β-strand	638-640	3	13
α-helix	642-644	3
α-helix	645-653	9
β-strand	654-657	4	14
β-strand	659-665	7	10
α-helix	672-675	4
β-strand	680-683	4	10
α-helix	688-690	3
β-strand	693-699	7	10
β-strand	708-714	7	10
α-helix	716-720	5
α-helix	726-740	15
α-helix	747-749	3
β-strand	751-754	4	10
α-helix	757-759	3
β-strand	767-770	4	14
β-strand	771	1	12
α-helix	777-783	7
β-strand	786	1	7
β-strand	790-792	3	7
α-helix	795-797	3
α-helix	805-821	17

Chain B: 45 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	63-64	2
β-strand	65	1	15
β-strand	82-86	5	15
β-strand	89-92	4	15
α-helix	107-120	14
α-helix	124-125	2
α-helix	127-134	8
β-strand	139-141	3	16
β-strand	150-152	3	16
α-helix	153-154	2
α-helix	161-166	6
α-helix	188-190	3
α-helix	191-197	7
α-helix	202-204	3
β-strand	211	1	17
α-helix	217-220	4
α-helix	225-228	4
β-strand	230	1	17
β-strand	272	1	18
α-helix	278-279	2
β-strand	284	1	18
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	341-359	19
α-helix	367-370	4
α-helix	380-382	3
β-strand	384-388	5	19
α-helix	392-404	13
β-strand	407-411	5	19
β-strand	423-424	2	20
β-strand	432-433	2	20
β-strand	438-440	3	21
α-helix	446-454	9
β-strand	459-460	2	21
α-helix	461-462	2
β-strand	467-469	3	22
α-helix	473	1
β-strand	474	1	22
α-helix	475-476	2
α-helix	477-497	21
α-helix	498-500	3
α-helix	503-505	3
β-strand	508	1	23
α-helix	509-524	16
α-helix	530-547	18
β-strand	554	1	24
β-strand	555	1	23
α-helix	561-564	4
α-helix	566-569	4
β-strand	572-574	3	21
α-helix	579-587	9
β-strand	591-593	3	19
β-strand	598-602	5	25
β-strand	608-612	5	25
β-strand	617-620	4	25
β-strand	622-625	4	19
α-helix	629-633	5
β-strand	638-640	3	25
α-helix	642-644	3
α-helix	645-653	9
β-strand	654-657	4	26
β-strand	660-665	6	22
α-helix	672-675	4
β-strand	680-684	5	22
α-helix	688-690	3
β-strand	693-699	7	22
β-strand	708-713	6	22
α-helix	718-721	4
α-helix	726-740	15
α-helix	747-749	3
β-strand	752-754	3	22
α-helix	757-759	3
β-strand	767-770	4	26
β-strand	771	1	24
α-helix	778-783	6
β-strand	786	1	19
β-strand	790-792	3	19
α-helix	795-797	3
α-helix	805-821	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1B	A, B	protein	796	Homo sapiens	Q8NB78 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4FWJ_1 Lysine-specific histone demethylase 1B (chains A, B)
GHMAKKKATETTDEDEDGGSEKKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLS
CGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPE
CRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLI
LPPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMN
RYFQPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEAL
TPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVI
IIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNP
VALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQD
VPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFA
QFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVT
VPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPP
SASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEV
PDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVT
GAYLSGVREASKIAAF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
FAD	Flavin-adenine dinucleotide	C27 H33 N9 O15 P2	2
PO4	Phosphate ion	O4 P	1

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

Primary citation

Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b. Zhang, Q., Qi, S., Xu, M. et al. Cell Res (2013) 23:225-241. DOI 10.1038/cr.2012.177 · PubMed

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
7XE3 2.82 Å, Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024)
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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