MolNFT v1 · #27663 · protein
Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and sah
1XQH · Histone-lysine N-methyltransferase, H3 lysine-4 specific: “Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53…”. X-ray diffraction, 1 ligand (SAH), 4 pockets (best druggability…
- PDB
- 1XQH
- Type
- protein
- Length
- 512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-4 specific; 9-mer peptide from tumor…
- EC
- 2.1.1.43
- UniProt
- Q8WTS6, P04637
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone-lysine N-methyltransferase, H3 lysine-4 specific (EC 2.1.1.43) | protein | 250 | 11% helix, 38% strand | Q8WTS6 |
| B, F | 9-mer peptide from tumor protein P53 | protein | 6 | 0% helix, 17% strand | P04637 |
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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.46 | 0.76 | 28 | SAH |
| 2 | 174 | 0.45 | 0.75 | 28 | SAH |
| 3 | 143 | 0.44 | 0.75 | 18 | empty |
| 4 | 87 | 0.32 | 0.72 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 610 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 601 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 601 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 1XQH · Crystal structure of a ternary complex of the methyltransferase SET9 (also known as… · the same entry in another collection · chain F against F, 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
- P04637 · AlphaFold monomer V2.0 prediction for cellular tumor antigen P53 (P04637) · a predicted model of the same protein · chain F against A, TM-score 0.61
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 P04637
- Elsewhere: RCSB PDB 1XQH · PDBe 1XQH · UniProt Q8WTS6 · UniProt P04637
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