4EZH: KDM6B

the crystal structure of KDM6B bound with H3K27me3 peptide. Determined by X-ray diffraction at 2.52 Å resolution. Released 8 Aug 2012.

Method: X-ray diffraction
Resolution: 2.52 Å
Organisms: Mus musculus, synthetic construct
Chains: 4
Atoms: 7,535
Mol. weight: 112.37 kDa
Ligands: NI, OGA, ZN
Released: 8 Aug 2012

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

Secondary structure: helices and β-sheets

4EZH contains 49 α-helices and 59 β-strands across 4 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, 28 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	1
α-helix	1195-1197	3
α-helix	1199-1206	8
β-strand	1212-1216	5	1
α-helix	1218-1221	4
α-helix	1226-1229	4
α-helix	1231-1237	7
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	1277-1293	17
β-strand	1325-1334	10	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	1371	1	5
β-strand	1376-1381	6	1
β-strand	1386-1390	5	6
α-helix	1393-1395	3
β-strand	1397-1405	9	1
β-strand	1408-1413	6	6
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	6
α-helix	1460	1
β-strand	1461-1464	4	1
β-strand	1469-1474	6	6
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	7
α-helix	1530-1556	27
β-strand	1562-1563	2	8
α-helix	1570-1572	3
β-strand	1573-1574	2	9
β-strand	1581-1582	2	9
β-strand	1585-1589	5	8
β-strand	1599-1601	3	8
α-helix	1603-1607	5
β-strand	1617-1620	4	8
α-helix	1624-1633	10
β-strand	1636	1	7

Chain B: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	1162-1164	3
α-helix	1178-1180	3
α-helix	1183-1185	3
β-strand	1187-1189	3	10
α-helix	1195-1197	3
α-helix	1199-1205	7
β-strand	1212-1216	5	10
α-helix	1218-1221	4
α-helix	1226-1229	4
α-helix	1231-1237	7
β-strand	1242-1249	8	10
β-strand	1257	1	11
β-strand	1264	1	11
β-strand	1267	1	12
β-strand	1271-1276	6	10
α-helix	1277-1295	19
β-strand	1325-1334	10	10
α-helix	1341-1346	6
α-helix	1347-1349	3
α-helix	1352-1354	3
β-strand	1361	1	13
α-helix	1362-1365	4
β-strand	1371	1	14
β-strand	1376-1381	6	10
β-strand	1386-1390	5	15
α-helix	1393-1395	3
β-strand	1397-1405	9	10
β-strand	1408-1413	6	15
α-helix	1415-1417	3
α-helix	1418-1427	10
β-strand	1437	1	12
α-helix	1441-1446	6
β-strand	1452-1456	5	15
α-helix	1460	1
β-strand	1461-1464	4	10
β-strand	1469-1474	6	15
β-strand	1478-1485	8	10
β-strand	1487	1	13
α-helix	1490-1505	16
α-helix	1514-1524	11
β-strand	1527	1	16
α-helix	1530-1556	27
β-strand	1562-1563	2	17
α-helix	1570-1572	3
β-strand	1573-1574	2	18
β-strand	1581-1582	2	18
β-strand	1585-1589	5	17
β-strand	1599-1601	3	17
α-helix	1603-1607	5
β-strand	1617-1620	4	17
α-helix	1624-1633	10
β-strand	1636	1	16

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	5
β-strand	33	1	1

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	26	1	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 6B	A, B	protein	486	Mus musculus	Q5NCY0 (AlphaFold model)
SYNTHESIZED methylation peptide	C, D	protein	11	synthetic construct	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4EZH_1 Lysine-specific demethylase 6B (chains A, B)
ESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIR
GLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTT
IAKYAQYQASSFQESLQEELEVLFQGPTKAARKSAPATGGGSSGSHHIIKFGTNIDLSDA
KRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFC
SVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQR
PGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHV
SWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNE
CDVEVFNILFVTSENGSRNTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLA
PASTSR

Sequence of entity 2 (C, D), FASTA

>4EZH_2 SYNTHESIZED methylation peptide (chains C, D)
AARKSAPATGG

Ligands and cofactors

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