4EZ4: Free KDM6B structure

free KDM6B structure. Determined by X-ray diffraction at 2.99 Å resolution. Released 8 Aug 2012.

Method: X-ray diffraction
Resolution: 2.99 Å
Organism: Mus musculus
Chains: 2
Atoms: 7,236
Mol. weight: 110.31 kDa
Ligands: ZN, NI, OGA
Released: 8 Aug 2012

Explore 4EZ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4EZ4 contains 49 α-helices and 46 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: 24 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	1162-1164	3
α-helix	1175-1177	3
α-helix	1178-1181	4
α-helix	1183-1186	4
β-strand	1187-1189	3	1
α-helix	1193-1197	5
α-helix	1199-1206	8
β-strand	1212-1216	5	1
α-helix	1218-1222	5
α-helix	1226-1229	4
α-helix	1231-1237	7
β-strand	1242-1248	7	1
β-strand	1257	1	2
β-strand	1264	1	2
β-strand	1267	1	3
β-strand	1271-1276	6	1
α-helix	1277-1294	18
β-strand	1326-1333	8	1
α-helix	1341-1344	4
α-helix	1352-1354	3
α-helix	1362-1365	4
β-strand	1377-1381	5	1
β-strand	1386-1390	5	4
α-helix	1393-1395	3
β-strand	1397-1405	9	1
β-strand	1408-1413	6	4
α-helix	1415-1417	3
α-helix	1418-1428	11
β-strand	1437	1	3
α-helix	1441-1446	6
β-strand	1452-1456	5	4
β-strand	1461-1464	4	1
α-helix	1465	1
β-strand	1469-1474	6	4
β-strand	1478-1485	8	1
α-helix	1490-1506	17
α-helix	1514-1524	11
α-helix	1530-1555	26
β-strand	1561-1563	3	5
α-helix	1570-1572	3
β-strand	1573-1574	2	6
β-strand	1581-1582	2	6
β-strand	1586-1590	5	5
β-strand	1598-1601	4	5
α-helix	1603-1609	7
β-strand	1617-1620	4	5
α-helix	1624-1632	9

Chain B: 25 helices, 23 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	7
α-helix	1193-1197	5
α-helix	1199-1206	8
β-strand	1212-1216	5	7
α-helix	1218-1222	5
α-helix	1231-1237	7
β-strand	1242-1249	8	7
β-strand	1257	1	8
β-strand	1264	1	8
β-strand	1267	1	9
β-strand	1271-1276	6	7
α-helix	1277-1293	17
β-strand	1325-1333	9	7
α-helix	1341-1346	6
α-helix	1352-1354	3
α-helix	1362-1364	3
β-strand	1377-1381	5	7
β-strand	1386-1390	5	10
α-helix	1393-1395	3
β-strand	1397-1405	9	7
β-strand	1408-1413	6	10
α-helix	1415-1417	3
α-helix	1418-1428	11
β-strand	1437	1	9
α-helix	1441-1446	6
β-strand	1452-1456	5	10
α-helix	1460	1
β-strand	1461-1464	4	7
α-helix	1465	1
β-strand	1469-1474	6	10
β-strand	1478-1485	8	7
α-helix	1490-1506	17
α-helix	1508-1510	3
α-helix	1514-1524	11
α-helix	1530-1555	26
β-strand	1561-1563	3	11
α-helix	1570-1572	3
β-strand	1573-1574	2	12
β-strand	1581-1582	2	12
β-strand	1586-1589	4	11
β-strand	1599-1601	3	11
α-helix	1603-1609	7
β-strand	1617-1620	4	11
α-helix	1624-1632	9

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

>4EZ4_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:

4EYU 2.3 Å, The free structure of the mouse C-terminal domain of KDM6B
4EZH 2.52 Å, the crystal structure of KDM6B bound with H3K27me3 peptide
9NQU 3.16 Å, KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate

Browse structure collections

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