Research workbench
Humanized mutant of the chaetomium thermophilum polycomb repressive complex 2 bound to the inhibitor GSK343
Analyse Humanized mutant of the chaetomium thermophilum polycomb repressive complex 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WFC
- Type
- protein
- Length
- 1,236 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein eed; Histone-lysine-N-methyltransferase EZH2, polycomb protein SUZ12…
- UniProt
- G0S8H7, G0SDW4, G0RYC6, P68431
- Ligands
- A97, ZN
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 460 | 9% helix, 40% strand | G0S8H7 |
| B | Histone-lysine-N-methyltransferase EZH2, polycomb protein SUZ12 chimera | protein | 769 | 38% helix, 13% strand | G0SDW4, G0RYC6 |
| D | Histone H3.1 | protein | 7 | 0% helix, 14% strand | P68431 |
Ligands and binding sites
- A97 · N-[(6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl) methyl]-6-[2-(4-methylpiperazin-1-yl)pyridin-4-yl]-1-(propan-2-yl)-1H-indazole-4-carboxamide · ligand · chains B
- ZN · Zinc ion · metal · 8 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.85 | 0.87 | 81 | empty |
| 2 | 1026 | 0.85 | 0.86 | 127 | empty |
| 3 | 1195 | 0.78 | 0.80 | 106 | empty |
| 4 | 350 | 0.63 | 0.78 | 45 | empty |
| 5 | 316 | 0.62 | 0.79 | 25 | A97 |
Interfaces
2 interfaces between chains.
- A–B · 5102 Ų buried · 68 hydrogen bonds · protein-protein
- A–D · 443 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 5WFC · Humanized mutant of the Chaetomium thermophilum Polycomb Repressive Complex 2 bound to… · the same entry in another collection · chain A against A, TM-score 1.00
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 G0S8H7
- Every structure of UniProt G0SDW4
- Every structure of UniProt G0RYC6
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 5WFC · PDBe 5WFC · UniProt G0S8H7 · UniProt G0SDW4 · UniProt G0RYC6 · UniProt P68431
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