Research workbench
Structure of human PRC2-EZH1 containing phosphorylated SUZ12
Analyse Structure of human PRC2-EZH1 containing phosphorylated SUZ12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TD5
- Type
- protein
- Length
- 1,992 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.994
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Histone-lysine N-methyltransferase EZH1; Polycomb protein EED; Polycomb protein SUZ12…
- EC
- 2.1.1.356
- UniProt
- Q92800, O75530, Q15022
- Ligands
- SAM, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.994 · 8 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EZH1 (EC 2.1.1.356) | protein | 497 | 29% helix, 16% strand | Q92800 |
| B | Polycomb protein EED | protein | 373 | 5% helix, 47% strand | O75530 |
| C, H | Polycomb protein SUZ12 | protein | 132 | 65% helix, 2% strand | Q15022 |
| D | Thr-lys-ala-ala-arg-met-ser-ala-pro-ser | protein | 10 | 0% helix, 10% strand | — |
| E, J | Thr-lys-ala-ala-arg-M3L-ser-ala-pro-ala | protein | 10 | 0% helix, 0% strand | — |
| F | Histone-lysine N-methyltransferase EZH1 (EC 2.1.1.356) | protein | 447 | 28% helix, 16% strand | Q92800 |
| G | Polycomb protein EED | protein | 372 | 6% helix, 47% strand | O75530 |
| I | Thr-lys-ala-ala-arg-met-ser-ala-pro-ser | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, D, F, I
- ZN · Zinc ion · metal · 16 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.87 | 0.93 | 44 | empty |
| 2 | 508 | 0.86 | 0.92 | 44 | empty |
| 3 | 680 | 0.81 | 0.85 | 85 | empty |
| 4 | 1002 | 0.80 | 0.82 | 93 | SAM |
| 5 | 1070 | 0.80 | 0.82 | 92 | SAM |
Interfaces
16 interfaces between chains.
- F–G · 4004 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3944 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 3178 Ų buried · 58 hydrogen bonds · protein-protein
- F–H · 3032 Ų buried · 44 hydrogen bonds · protein-protein
- B–G · 1015 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation, phosphorylation).
Compared structures
- O75530 · AlphaFold monomer V2.0 prediction for polycomb protein eed (O75530) · a predicted model of the same protein · chain G 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 F against A, TM-score 0.98
- Q15022 · AlphaFold monomer V2.0 prediction for polycomb protein SUZ12 (Q15022) · a predicted model of the same protein · chain C against A, TM-score 0.95
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
- Elsewhere: RCSB PDB 7TD5 · PDBe 7TD5 · UniProt Q92800 · UniProt O75530 · UniProt Q15022
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