Research workbench
Crystal structure of eed in complex with H3K27ME3 peptide and 3- (BENZO[D][1,3]DIOXOL-4-YLMETHYL)PIPERIDINE-1-carboximidamide
Analyse Crystal structure of eed in complex with H3K27ME3 peptide and 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U5T
- Type
- protein
- Length
- 750 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
- 7W7, YT3
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 348 | 3% helix, 48% strand | O75530 |
| B | Polycomb protein eed | protein | 348 | 4% helix, 48% strand | O75530 |
| C | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 26 | 73% helix, 0% strand | Q15910 |
| D | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 28 | 75% helix, 0% strand | Q15910 |
Ligands and binding sites
- 7W7 · (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide · ligand · 2 copies · chains A, B
- YT3 · Yttrium (III) ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.86 | 0.94 | 44 | empty |
| 2 | 409 | 0.86 | 0.94 | 43 | empty |
| 3 | 96 | 0.54 | 0.84 | 14 | 7W7 |
| 4 | 100 | 0.52 | 0.83 | 14 | 7W7 |
| 5 | 107 | 0.41 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1411 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1304 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U5T · Crystal structure of EED in complex with H3K27Me3 peptide and… · 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 1.00
- Q15910 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EZH2 (Q15910) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 5U5T · PDBe 5U5T · UniProt O75530 · UniProt Q15910
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