Research workbench
Human polycomb repressive complex 2 in complex with GSK126 inhibitor
Analyse Human polycomb repressive complex 2 in complex with GSK126 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WG6
- Type
- protein
- Length
- 1,650 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EZH2,POLYCOMB protein SUZ12 (E.C.2.1.1.43) chimera…
- EC
- 2.1.1.43
- UniProt
- Q15910, Q15022, O75530
- Ligands
- A9G, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EZH2,POLYCOMB protein SUZ12 (E.C.2.1.1.43) chimera (EC 2.1.1.43) | protein | 517 | 36% helix, 15% strand | Q15910, Q15022 |
| B | Polycomb protein eed | protein | 355 | 4% helix, 41% strand | O75530 |
| C | Histone-lysine N-methyltransferase EZH2,POLYCOMB protein SUZ12 (E.C.2.1.1.43) chimera (EC 2.1.1.43) | protein | 504 | 34% helix, 12% strand | Q15910, Q15022 |
| D | Polycomb protein eed | protein | 274 | 5% helix, 38% strand | O75530 |
Ligands and binding sites
- A9G · 1-[(2S)-butan-2-yl]-N-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-indole-4-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · 16 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.86 | 0.95 | 37 | empty |
| 2 | 340 | 0.85 | 0.94 | 35 | empty |
| 3 | 417 | 0.74 | 0.84 | 62 | empty |
| 4 | 188 | 0.73 | 0.90 | 40 | empty |
| 5 | 72 | 0.70 | 0.95 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4223 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2746 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 105 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 94 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 34 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5WG6 · Human Polycomb Repressive Complex 2 in complex with GSK126 inhibitor · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.74
- Q15022 · AlphaFold monomer V2.0 prediction for polycomb protein SUZ12 (Q15022) · a predicted model of the same protein · chain C against A, TM-score 0.27
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 Q15910
- Every structure of UniProt Q15022
- Every structure of UniProt O75530
- Elsewhere: RCSB PDB 5WG6 · PDBe 5WG6 · UniProt Q15910 · UniProt Q15022 · UniProt O75530
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