Research workbench
Structure of human polycomb repressive complex 2 (PRC2) with oncogenic histone H3K27M peptide
Analyse Structure of human polycomb repressive complex 2 (PRC2) with oncogenic histone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HYN
- Type
- protein
- Length
- 4,311 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EZH2; Polycomb protein eed; Polycomb protein SUZ12…
- EC
- 2.1.1.43
- UniProt
- Q15910, O75530, Q15022
- Ligands
- SAH, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 11 distinct chains · 30% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 581 | 31% helix, 13% strand | Q15910 |
| B, G, L, R | Polycomb protein eed | protein | 365 | 4% helix, 47% strand | O75530 |
| C, M, S | Polycomb protein SUZ12 | protein | 125 | 57% helix, 2% strand | Q15022 |
| D, I, O, T | H3K27M | protein | 9 | 0% helix, 11% strand | — |
| E | JARID2 K116ME3 | protein | 11 | 0% helix, 0% strand | — |
| F | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 568 | 31% helix, 14% strand | Q15910 |
| H | Polycomb protein SUZ12 | protein | 124 | 61% helix, 2% strand | Q15022 |
| J, U | JARID2 K116ME3 | protein | 10 | 0% helix, 0% strand | — |
| K | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 562 | 31% helix, 14% strand | Q15910 |
| P | JARID2 K116ME3 | protein | 9 | 0% helix, 0% strand | — |
| Q | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 565 | 32% helix, 14% strand | Q15910 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, F, K, Q
- ZN · Zinc ion · metal · 32 copies · chains A, F, K, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.87 | 0.94 | 41 | empty |
| 2 | 388 | 0.86 | 0.95 | 39 | empty |
| 3 | 377 | 0.86 | 0.95 | 43 | empty |
| 4 | 361 | 0.86 | 0.95 | 43 | empty |
| 5 | 390 | 0.84 | 0.92 | 47 | empty |
Interfaces
37 interfaces between chains.
- F–G · 4412 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 4342 Ų buried · 59 hydrogen bonds · protein-protein
- Q–R · 4325 Ų buried · 57 hydrogen bonds · protein-protein
- K–L · 4266 Ų buried · 58 hydrogen bonds · protein-protein
- F–H · 3145 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 5HYN · Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M… · the same entry in another collection · chain K against K, 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 Q15910
- Every structure of UniProt O75530
- Every structure of UniProt Q15022
- Elsewhere: RCSB PDB 5HYN · PDBe 5HYN · UniProt Q15910 · UniProt O75530 · UniProt Q15022
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