Research workbench
Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the extended active state
Analyse Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the extended… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C24
- Type
- protein
- Length
- 1,772 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein SUZ12; Protein jumonji; Histone-lysine N-methyltransferase EZH2…
- EC
- 2.1.1.43
- UniProt
- Q15022, Q92833, Q15910, O75530, Q09028, Q6ZN18
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 12 distinct chains · 18% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein SUZ12 | protein | 123 | 11% helix, 12% strand | Q15022 |
| B | Protein jumonji | protein | 7 | 0% helix, 0% strand | Q92833 |
| E | Protein jumonji | protein | 27 | 26% helix, 0% strand | Q92833 |
| K | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 325 | 21% helix, 16% strand | Q15910 |
| L | Polycomb protein eed | protein | 362 | 3% helix, 37% strand | O75530 |
| M | Polycomb protein SUZ12 | protein | 122 | 60% helix, 3% strand | Q15022 |
| N | Histone-binding protein RBBP4 | protein | 386 | 8% helix, 33% strand | Q09028 |
| O | JARID2-substrate | protein | 7 | 0% helix, 14% strand | — |
| P | Zinc finger protein AEBP2 | protein | 64 | 23% helix, 0% strand | Q6ZN18 |
| Q | Polycomb protein SUZ12 | protein | 66 | 33% helix, 0% strand | Q15022 |
| Z | SUZ12 | protein | 135 | 2% helix, 15% strand | — |
| C | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 148 | 53% helix, 3% strand | Q15910 |
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 | 423 | 0.86 | 0.94 | 46 | empty |
| 2 | 883 | 0.80 | 0.83 | 89 | empty |
| 3 | 271 | 0.80 | 0.92 | 45 | empty |
| 4 | 720 | 0.79 | 0.83 | 88 | empty |
| 5 | 473 | 0.77 | 0.85 | 31 | empty |
Interfaces
31 interfaces between chains.
- L–C · 2901 Ų buried · 28 hydrogen bonds · protein-protein
- K–M · 2591 Ų buried · 25 hydrogen bonds · protein-protein
- N–Q · 1675 Ų buried · 21 hydrogen bonds · protein-protein
- A–N · 1487 Ų buried · 15 hydrogen bonds · protein-protein
- N–P · 1307 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, methylation).
Compared structures
- 6C24 · Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Extended Active State · the same entry in another collection · chain C against C, 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 Q15022
- Every structure of UniProt Q92833
- Every structure of UniProt Q15910
- Every structure of UniProt O75530
- Every structure of UniProt Q09028
- Every structure of UniProt Q6ZN18
- Elsewhere: RCSB PDB 6C24 · PDBe 6C24 · UniProt Q15022 · UniProt Q92833 · UniProt Q15910 · UniProt O75530 · UniProt Q09028 · UniProt Q6ZN18
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