5K0M: Polycomb protein EED

Targeting the PRC2 complex through a novel protein-protein interaction inhibitor of EED. Determined by X-ray diffraction at 1.83 Å resolution. Released 25 Jan 2017.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,318
Mol. weight: 43.42 kDa
Ligands: 6PU
Released: 25 Jan 2017

Explore 5K0M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K0M contains 8 α-helices and 29 β-strands across 1 chain. 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: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	83-89	7	1
β-strand	96-101	6	2
α-helix	105-106	2
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	171-175	5	3
β-strand	182-187	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
α-helix	282-284	3
α-helix	288-291	4
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
α-helix	396-398	3
α-helix	399	1
β-strand	400-404	5	7
β-strand	413-418	6	1
β-strand	424-429	6	1
β-strand	433-438	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polycomb protein EED	A	protein	372	Homo sapiens	O75530 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5K0M_1 Polycomb protein EED (chains A)
VPRGSHMKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQ
GEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGH
GNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGE
KIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYV
DCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFS
MDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVC
DDASIWRWDRLR

Ligands and cofactors

ID	Name	Formula	Copies
6PU	(3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-{4-[4-(methy…	C26 H35 F N4 O2 S	1

Primary citation

The EED protein-protein interaction inhibitor A-395 inactivates the PRC2 complex. He, Y., Selvaraju, S., Curtin, M.L. et al. Nat Chem Biol (2017) 13:389-395. DOI 10.1038/nchembio.2306 · 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

Browse structure collections

About this viewer

MolViewer shows 5K0M directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.