5U62: EED

Crystal structure of EED in complex with H3K27Me3 peptide and 6-(benzo[d][1,3]dioxol-4-ylmethyl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine. Determined by X-ray diffraction at 1.9 Å resolution. Released 11 Jan 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,983
Mol. weight: 93.03 kDa
Ligands: 7WD, YT3
Released: 11 Jan 2017

Explore 5U62 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U62 contains 13 α-helices and 58 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: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	82-89	8	1
α-helix	94-95	2
β-strand	96-101	6	2
α-helix	106	1
α-helix	110	1
β-strand	111-117	7	2
β-strand	120-126	7	2
β-strand	132-139	8	2
β-strand	147-154	8	3
β-strand	161-167	7	3
β-strand	172-176	5	3
β-strand	181-186	6	3
β-strand	193-198	6	4
β-strand	205-210	6	4
β-strand	215-219	5	4
β-strand	224-229	6	4
β-strand	239-244	6	5
β-strand	250-255	6	5
β-strand	260-264	5	5
α-helix	268-279	12
β-strand	292-294	3	4
β-strand	299-301	3	5
β-strand	311-315	5	6
β-strand	318-322	5	6
β-strand	327-333	7	6
α-helix	340-342	3
β-strand	350-357	8	6
β-strand	368-370	3	7
β-strand	376-380	5	7
β-strand	386-390	5	7
β-strand	402-404	3	7
β-strand	413-418	6	1
β-strand	424-429	6	1
β-strand	433-439	7	1

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	82-89	8	8
α-helix	94-95	2
β-strand	96-101	6	9
α-helix	106	1
β-strand	111-117	7	9
β-strand	120-126	7	9
β-strand	132-139	8	9
β-strand	147-154	8	10
β-strand	161-167	7	10
β-strand	172-176	5	10
β-strand	181-186	6	10
β-strand	193-198	6	11
β-strand	205-210	6	11
β-strand	215-219	5	11
β-strand	224-229	6	11
β-strand	239-244	6	12
β-strand	250-255	6	12
β-strand	260-264	5	12
α-helix	268-279	12
α-helix	288-289	2
β-strand	292-294	3	11
β-strand	299-301	3	12
β-strand	311-315	5	13
β-strand	318-322	5	13
β-strand	327-333	7	13
β-strand	350-357	8	13
β-strand	368-370	3	14
β-strand	376-380	5	14
β-strand	386-390	5	14
β-strand	402-404	3	14
β-strand	413-418	6	8
β-strand	424-429	6	8
β-strand	433-439	7	8

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	44-62	19
α-helix	65-67	3

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	42-62	21
α-helix	65-67	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polycomb protein EED	A, B	protein	367	Homo sapiens	O75530 (AlphaFold model)
Histone-lysine N-methyltransferase EZH2	C, D	protein	30	Homo sapiens	Q15910 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5U62_1 Polycomb protein EED (chains A, B)
GKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRL
LQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAIN
ELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSC
GMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRW
LGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQ
KMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASI
WRWDRLR

Sequence of entity 2 (C, D), FASTA

>5U62_2 Histone-lysine N-methyltransferase EZH2 (chains C, D)
KSMFSSNRQKILERTEILNQEWKQRRIQPV

Ligands and cofactors

ID	Name	Formula	Copies
7WD	(6S)-6-[(2H-1,3-benzodioxol-4-yl)methyl]-5,6,7,8-tetrahydroimidazo[1,5-a]pyridi…	C15 H17 N3 O2	2
YT3	Yttrium (III) ion	Y	2

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

Primary citation

Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase. Lingel, A., Sendzik, M., Huang, Y. et al. J Med Chem (2017) 60:415-427. DOI 10.1021/acs.jmedchem.6b01473 · PubMed

Other PDB entries of the same protein (UniProt O75530 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5U69 1.28 Å, Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-d…
5U8F 1.34 Å, Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-i…
5U8A 1.45 Å, Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl…
6SFB 1.52 Å, EED in complex with a triazolopyrimidine
3K26 1.58 Å, Complex structure of EED and trimethylated H3K4
5U5T 1.6 Å, Crystal structure of EED in complex with H3K27Me3 peptide and…
7QK4 1.6 Å, EED in complex with PRC2 allosteric inhibitor compound 22 (MAK683)
7P3C 1.61 Å, EED in complex with compound 4
6V3Y 1.63 Å, Crystal structure of EED in complex with PALI1-K1219me3 peptide
5U6D 1.64 Å, Polycomb protein EED in complex with inhibitor: 2-[4-(4-{(3S,4R)-4-(dimethylamino)-1-[(2-…
6V3X 1.7 Å, Crystal structure of EED in complex with PALI1-K1241me3 peptide
5TTW 1.74 Å, Crystal Structure of EED in Complex with UNC4859

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