MolNFT v1 · #180217 · protein
PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome
7KSR · Histone-lysine N-methyltransferase EZH1: “PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.84). MolNFT v1 #180217 on GenesisL1: 3D structure, binding sites…
- PDB
- 7KSR
- Type
- protein
- Length
- 1,524 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EZH1; Histone-binding protein RBBP4; Polycomb protein…
- EC
- 2.1.1.356
- UniProt
- Q92800, Q09028, Q15022, O75530
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EZH1 (EC 2.1.1.356) | protein | 395 | 24% helix, 15% strand | Q92800 |
| D | Histone-binding protein RBBP4 | protein | 367 | 8% helix, 43% strand | Q09028 |
| C | Polycomb protein SUZ12 | protein | 397 | 30% helix, 17% strand | Q15022 |
| B | Polycomb protein eed | protein | 365 | 5% helix, 40% strand | O75530 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.84 | 0.93 | 39 | empty |
| 2 | 726 | 0.77 | 0.82 | 82 | empty |
| 3 | 534 | 0.76 | 0.83 | 58 | empty |
| 4 | 477 | 0.75 | 0.84 | 36 | empty |
| 5 | 90 | 0.72 | 0.95 | 20 | empty |
Interfaces
4 interfaces between chains.
- D–C · 3342 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 3276 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 3093 Ų buried · 26 hydrogen bonds · protein-protein
- C–B · 735 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7KSR · PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome · the same entry in another collection · chain B against B, 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 0.98
- Q09028 · AlphaFold monomer V2.0 prediction for histone-binding protein RBBP4 (Q09028) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q92800 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EZH1 (Q92800) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q15022 · AlphaFold monomer V2.0 prediction for polycomb protein SUZ12 (Q15022) · a predicted model of the same protein · chain C against A, TM-score 0.44
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 Q92800
- Every structure of UniProt Q09028
- Every structure of UniProt Q15022
- Every structure of UniProt O75530
- Elsewhere: RCSB PDB 7KSR · PDBe 7KSR · UniProt Q92800 · UniProt Q09028 · UniProt Q15022 · UniProt O75530
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