Research workbench
Crystal structure of a ternary complex of the human histone methyltransferase pr-SET7 (also known as SET8)
Analyse Crystal structure of a ternary complex of the human histone methyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BQZ
- Type
- protein
- Length
- 342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SET8 protein; Histone H4
- EC
- 2.1.1.43
- UniProt
- Q86W83, P62805
- Ligands
- SAH
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | SET8 protein (EC 2.1.1.43) | protein | 161 | 27% helix, 35% strand | Q86W83 |
| B, F | Histone H4 | protein | 10 | 0% helix, 20% strand | P62805 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.56 | 0.78 | 37 | SAH |
| 2 | 162 | 0.47 | 0.76 | 28 | SAH |
| 3 | 118 | 0.39 | 0.75 | 25 | empty |
| 4 | 79 | 0.34 | 0.75 | 11 | empty |
| 5 | 54 | 0.33 | 0.78 | 19 | empty |
Interfaces
3 interfaces between chains.
- E–F · 966 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 880 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 350 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2BQZ · Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7… · the same entry in another collection · chain B against B, TM-score 1.00
- P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain F against A, TM-score 0.31
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 Q86W83
- Every structure of UniProt P62805
- Elsewhere: RCSB PDB 2BQZ · PDBe 2BQZ · UniProt Q86W83 · UniProt P62805
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