MolNFT v1 · #16804 · protein
Crystal structure of a ternary complex of the human histone methyltransferase SET7/9
1O9S · Histone-lysine N-methyltransferase, H3 lysine-4 specific: “Crystal structure of a ternary complex of the human histone methyltransferase SET7/9”. X-ray diffraction, 1 ligand (SAH), 3 pockets (best druggability 0.55). MolNFT v1…
- PDB
- 1O9S
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-4 specific; Gene fragment for histone H3
- EC
- 2.1.1.43
- UniProt
- Q8WTS6, Q16776
- Ligands
- SAH
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone-lysine N-methyltransferase, H3 lysine-4 specific (EC 2.1.1.43) | protein | 250 | 11% helix, 38% strand | Q8WTS6 |
| K | Gene fragment for histone H3 | protein | 10 | 0% helix, 10% strand | Q16776 |
| L | Gene fragment for histone H3 | protein | 6 | 0% helix, 17% strand | Q16776 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, K, B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.55 | 0.77 | 31 | empty |
| 2 | 183 | 0.46 | 0.75 | 33 | SAH |
| 3 | 172 | 0.45 | 0.75 | 26 | SAH |
Interfaces
4 interfaces between chains.
- A–K · 681 Ų buried · 14 hydrogen bonds · protein-protein
- B–L · 656 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 301 Ų buried · 1 hydrogen bond · protein-protein
- B–K · 129 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 1O9S · Crystal structure of a ternary complex of the human histone methyltransferase SET7/9 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WTS6 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD7 (Q8WTS6) · a predicted model of the same protein · chain A 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 Q8WTS6
- Every structure of UniProt Q16776
- Elsewhere: RCSB PDB 1O9S · PDBe 1O9S · UniProt Q8WTS6 · UniProt Q16776
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