Research workbench
Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2
Analyse Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KSO
- Type
- protein
- Length
- 1,690 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EZH1; Polycomb protein eed; Polycomb protein SUZ12…
- EC
- 2.1.1.356
- UniProt
- Q92800, O75530, Q15022, Q09028, Q6ZN18, Q92833
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EZH1 (EC 2.1.1.356) | protein | 395 | 26% helix, 15% strand | Q92800 |
| B | Polycomb protein eed | protein | 365 | 5% helix, 39% strand | O75530 |
| C | Polycomb protein SUZ12 | protein | 420 | 31% helix, 21% strand | Q15022 |
| D | Histone-binding protein RBBP4 | protein | 387 | 9% helix, 40% strand | Q09028 |
| E | Zinc finger protein AEBP2 | protein | 100 | 26% helix, 20% strand | Q6ZN18 |
| F | Protein jumonji | protein | 23 | 43% helix, 4% strand | Q92833 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 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 | 1095 | 0.85 | 0.86 | 115 | empty |
| 2 | 293 | 0.83 | 0.93 | 34 | empty |
| 3 | 904 | 0.80 | 0.83 | 89 | empty |
| 4 | 799 | 0.76 | 0.80 | 95 | empty |
| 5 | 404 | 0.75 | 0.85 | 33 | empty |
Interfaces
12 interfaces between chains.
- C–D · 4134 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3354 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 3149 Ų buried · 28 hydrogen bonds · protein-protein
- C–E · 1436 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1059 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7KSO · Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2 · the same entry in another collection · chain E against E, 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 0.98
- 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
- Q6ZN18 · AlphaFold monomer V2.0 prediction for zinc finger protein AEBP2 (Q6ZN18) · a predicted model of the same protein · chain E against A, TM-score 0.93
- Q15022 · AlphaFold monomer V2.0 prediction for polycomb protein SUZ12 (Q15022) · a predicted model of the same protein · chain C against A, TM-score 0.93
- Q92833 · AlphaFold monomer V2.0 prediction for protein jumonji (Q92833) · a predicted model of the same protein · chain F against A, TM-score 0.40
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 O75530
- Every structure of UniProt Q15022
- Every structure of UniProt Q09028
- Every structure of UniProt Q6ZN18
- Every structure of UniProt Q92833
- Elsewhere: RCSB PDB 7KSO · PDBe 7KSO · UniProt Q92800 · UniProt O75530 · UniProt Q15022 · UniProt Q09028 · UniProt Q6ZN18 · UniProt Q92833
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