4GUT: LSD2-NPAC

Crystal structure of LSD2-NPAC. Determined by X-ray diffraction at 2.0 Å resolution. Released 16 Jan 2013.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,390
Mol. weight: 101.9 kDa
Ligands: FAD, ZN
Released: 16 Jan 2013

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

Secondary structure: helices and β-sheets

4GUT contains 49 α-helices and 40 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: 48 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	1
β-strand	53	1	2
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	107-119	13
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	161-166	6
α-helix	184-186	3
α-helix	188-190	3
α-helix	191-195	5
β-strand	211	1	4
α-helix	217-219	3
α-helix	225-227	3
β-strand	230	1	4
β-strand	272	1	5
α-helix	273-274	2
α-helix	277-279	3
β-strand	284	1	5
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	371-373	3
α-helix	378-380	3
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	467-468	2	9
α-helix	469	1
α-helix	473	1
β-strand	474	1	9
α-helix	475-476	2
α-helix	477-497	21
α-helix	498-500	3
α-helix	503-505	3
β-strand	508	1	10
α-helix	509-523	15
α-helix	526-529	4
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	580-587	8
β-strand	592-593	2	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	660-665	6	9
α-helix	672-675	4
β-strand	680-683	4	9
α-helix	688-690	3
β-strand	693-699	7	9
β-strand	708-713	6	9
α-helix	716-722	7
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	805-820	16

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	220-222	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1B	A	protein	776	Homo sapiens	Q8NB78 (AlphaFold model)
Putative oxidoreductase GLYR1	B	protein	124	Homo sapiens	Q49A26 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4GUT_1 Lysine-specific histone demethylase 1B (chains A)
PLGSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDG
YDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKT
YRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPD
CVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRP
DVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCV
QEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGI
KVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCD
LIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGI
QFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKL
AEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEK
KMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKH
SVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMA
YSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

Sequence of entity 2 (B), FASTA

>4GUT_2 Putative oxidoreductase GLYR1 (chains B)
PLGSPEFSERGSKSPLKRAQEQSPRKRGRPPKDEKDLTIPESSTVKGMMAGPMAAFKWQP
TASEPVKDADPHFHHFLLSQTEKPAVCYQAITKKLKICEEETGSTSIQAADSTAVNGSIT
PTDK

Ligands and cofactors

ID	Name	Formula	Copies
FAD	Flavin-adenine dinucleotide	C27 H33 N9 O15 P2	1
ZN	Zinc ion	Zn	3

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

Primary citation

LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Fang, R., Chen, F., Dong, Z. et al. Mol Cell (2013) 49:558-570. DOI 10.1016/j.molcel.2012.11.019 · 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
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)
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

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