MolNFT v1 · #135675 · protein
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
5U62 · Polycomb protein eed: “Crystal structure of eed in complex with H3K27ME3 peptide and 6…”. X-ray diffraction, 2 ligands (7WD, YT3), 8 pockets (best druggability 0.86). MolNFT v1 #135675 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5U62
- Type
- protein
- Length
- 757 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
- 7WD, YT3
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 349 | 4% helix, 48% strand | O75530 |
| B | Polycomb protein eed | protein | 354 | 3% helix, 47% 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
- 7WD · (6S)-6-[(2H-1,3-benzodioxol-4-yl)methyl]-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine · ligand · 2 copies · chains A, B
- YT3 · Yttrium (III) ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.86 | 0.94 | 45 | empty |
| 2 | 359 | 0.85 | 0.94 | 45 | empty |
| 3 | 90 | 0.56 | 0.85 | 12 | 7WD |
| 4 | 90 | 0.55 | 0.85 | 11 | 7WD |
| 5 | 77 | 0.42 | 0.79 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1393 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1290 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 41 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U62 · 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 A 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 0.89
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 5U62 · PDBe 5U62 · UniProt O75530 · UniProt Q15910
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