4EYU: Lysine-specific demethylase 6B

The free structure of the mouse C-terminal domain of KDM6B. Determined by X-ray diffraction at 2.3 Å resolution. Released 8 Aug 2012.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Mus musculus
Chains: 2
Atoms: 7,525
Mol. weight: 110.31 kDa
Ligands: ZN, NI, OGA
Released: 8 Aug 2012

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

Secondary structure: helices and β-sheets

4EYU contains 50 α-helices and 54 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: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	1162-1164	3
α-helix	1167-1169	3
α-helix	1178-1181	4
α-helix	1183-1186	4
β-strand	1187-1189	3	1
α-helix	1193-1197	5
α-helix	1199-1205	7
β-strand	1212-1216	5	1
α-helix	1218-1222	5
α-helix	1226-1229	4
α-helix	1231-1238	8
β-strand	1242-1249	8	1
β-strand	1257	1	2
β-strand	1264	1	2
β-strand	1267	1	3
β-strand	1271-1276	6	1
α-helix	1277-1300	24
β-strand	1325-1333	9	1
α-helix	1341-1346	6
α-helix	1347-1349	3
α-helix	1352-1354	3
β-strand	1361	1	4
α-helix	1362-1365	4
β-strand	1377-1381	5	1
β-strand	1386-1390	5	5
α-helix	1393-1395	3
β-strand	1397-1405	9	1
α-helix	1407	1
β-strand	1408-1413	6	5
α-helix	1415-1417	3
α-helix	1418-1427	10
β-strand	1437	1	3
α-helix	1441-1446	6
β-strand	1452-1456	5	5
β-strand	1461-1464	4	1
β-strand	1469-1474	6	5
β-strand	1478-1485	8	1
β-strand	1487	1	4
α-helix	1490-1505	16
α-helix	1514-1524	11
β-strand	1527	1	6
α-helix	1530-1555	26
β-strand	1561-1563	3	7
α-helix	1566-1567	2
β-strand	1573-1574	2	8
β-strand	1581-1582	2	8
β-strand	1585-1590	6	7
β-strand	1598-1601	4	7
α-helix	1603-1609	7
β-strand	1617-1620	4	7
α-helix	1624-1633	10
β-strand	1636	1	6

Chain B: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	1162-1164	3
α-helix	1167-1169	3
α-helix	1178-1181	4
α-helix	1183-1185	3
β-strand	1187-1189	3	9
α-helix	1193-1197	5
α-helix	1199-1205	7
β-strand	1212-1216	5	9
α-helix	1218-1221	4
α-helix	1226-1229	4
α-helix	1231-1237	7
β-strand	1242-1249	8	9
β-strand	1257	1	10
β-strand	1264	1	10
β-strand	1267	1	11
α-helix	1268-1269	2
β-strand	1271-1276	6	9
α-helix	1277-1299	23
β-strand	1325-1333	9	9
α-helix	1341-1346	6
α-helix	1347-1349	3
α-helix	1352-1354	3
β-strand	1361	1	12
α-helix	1362-1365	4
β-strand	1377-1381	5	9
β-strand	1386-1390	5	13
α-helix	1393-1395	3
β-strand	1397-1405	9	9
β-strand	1408-1413	6	13
α-helix	1415-1417	3
α-helix	1418-1427	10
β-strand	1437	1	11
α-helix	1441-1446	6
β-strand	1452-1456	5	13
β-strand	1461-1464	4	9
β-strand	1469-1474	6	13
β-strand	1478-1485	8	9
β-strand	1487	1	12
α-helix	1490-1505	16
α-helix	1514-1524	11
β-strand	1527	1	14
α-helix	1530-1555	26
β-strand	1561-1563	3	15
α-helix	1570-1572	3
β-strand	1573-1574	2	16
β-strand	1581-1582	2	16
β-strand	1586-1590	5	15
β-strand	1598-1601	4	15
α-helix	1603-1609	7
β-strand	1617-1620	4	15
α-helix	1624-1633	10
β-strand	1636	1	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 6B	A, B	protein	486	Mus musculus	Q5NCY0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4EYU_1 Lysine-specific demethylase 6B (chains A, B)
ESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIR
GLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTT
IAKYAQYQASSFQESLQEELEVLFQGPTKAARKSAPATGGGSSGSHHIIKFGTNIDLSDA
KRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFC
SVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQR
PGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHV
SWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNE
CDVEVFNILFVTSENGSRNTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLA
PASTSR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
NI	Nickel (II) ion	Ni	2
OGA	N-oxalylglycine	C4 H5 N O5	2

Primary citation

A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Kruidenier, L., Chung, C.W., Cheng, Z. et al. Nature (2012) 488:404-408. DOI 10.1038/nature11262 · PubMed

Other PDB entries of the same protein (UniProt Q5NCY0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4EZH 2.52 Å, the crystal structure of KDM6B bound with H3K27me3 peptide
4EZ4 2.99 Å, free KDM6B structure
9NQU 3.16 Å, KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate

Browse structure collections

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