Research workbench
Eed in complex with an allosteric PRC2 inhibitor EED666
Analyse Eed in complex with an allosteric PRC2 inhibitor EED666 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H14
- Type
- protein
- Length
- 780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein eed; Histone-lysine N-methyltransferase EZH2
- EC
- 2.1.1.43
- UniProt
- O75530, Q15910
- Ligands
- LQB
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 365 | 4% helix, 46% strand | O75530 |
| B | Polycomb protein eed | protein | 357 | 3% helix, 47% strand | O75530 |
| C, D | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 29 | 76% helix, 0% strand | Q15910 |
Ligands and binding sites
- LQB · 2-[3-(3,5-dimethylpyrazol-1-yl)-4-nitro-phenyl]-3,4-dihydro-1H-isoquinoline · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.86 | 0.94 | 43 | empty |
| 2 | 424 | 0.86 | 0.94 | 40 | empty |
| 3 | 108 | 0.61 | 0.86 | 16 | empty |
| 4 | 89 | 0.57 | 0.86 | 19 | GOL |
| 5 | 87 | 0.53 | 0.84 | 12 | LQB |
Interfaces
5 interfaces between chains.
- A–D · 1531 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1505 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 51 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5H14 · EED in complex with an allosteric PRC2 inhibitor EED666 · the same entry in another collection · chain D against D, TM-score 1.00
- O75530 · AlphaFold monomer V2.0 prediction for polycomb protein eed (O75530) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q15910 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EZH2 (Q15910) · a predicted model of the same protein · chain D against A, TM-score 0.87
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O75530
- Every structure of UniProt Q15910
- Elsewhere: RCSB PDB 5H14 · PDBe 5H14 · UniProt O75530 · UniProt Q15910
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