Research workbench
Structural insights into lysine multiple methylation by set domain methyltransferases, SET8-Y334F / H4-LYS20ME2 / adohcy
Analyse Structural insights into lysine multiple methylation by set domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F9X
- Type
- protein
- Length
- 675 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD8; Histone H4
- EC
- 2.1.1.43
- UniProt
- Q9NQR1, P62805
- Ligands
- SAH
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Histone-lysine N-methyltransferase SETD8 (EC 2.1.1.43) | protein | 160 | 26% helix, 34% strand | Q9NQR1 |
| D | Histone-lysine N-methyltransferase SETD8 (EC 2.1.1.43) | protein | 161 | 28% helix, 35% strand | Q9NQR1 |
| E, G | Histone H4 | protein | 9 | 0% helix, 33% strand | P62805 |
| F, H | Histone H4 | protein | 8 | 0% helix, 25% strand | P62805 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, F, G, B, E, C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.73 | 0.79 | 62 | SAH |
| 2 | 696 | 0.72 | 0.79 | 60 | SAH |
| 3 | 336 | 0.68 | 0.82 | 34 | SAH |
| 4 | 300 | 0.56 | 0.77 | 36 | empty |
| 5 | 190 | 0.52 | 0.78 | 28 | empty |
Interfaces
10 interfaces between chains.
- B–E · 935 Ų buried · 13 hydrogen bonds · protein-protein
- D–H · 883 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 864 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 843 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 532 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 3F9X · Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9NQR1 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase KMT5A (Q9NQR1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9NQR1
- Every structure of UniProt P62805
- Elsewhere: RCSB PDB 3F9X · PDBe 3F9X · UniProt Q9NQR1 · UniProt P62805
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