MolNFT v1 · #111327 · protein
ASH1L wild-type set domain in complex with S-adenosyl methionine (SAM)
4YNM · Histone-lysine N-methyltransferase ASH1L: “ASH1L wild-type set domain in complex with S-adenosyl methionine (SAM)”. X-ray diffraction, 2 ligands (SAM, ZN), 4 pockets (best druggability 0.78). MolNFT v1 #111327 on GenesisL1: 3D…
- PDB
- 4YNM
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase ASH1L
- EC
- 2.1.1.43
- UniProt
- Q9NR48
- Ligands
- SAM, ZN
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase ASH1L (EC 2.1.1.43) | protein | 215 | 12% helix, 30% strand | Q9NR48 |
| B | Histone-lysine N-methyltransferase ASH1L (EC 2.1.1.43) | protein | 196 | 13% helix, 30% strand | Q9NR48 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.78 | 0.80 | 78 | empty |
| 2 | 189 | 0.66 | 0.85 | 33 | SAM |
| 3 | 207 | 0.66 | 0.84 | 36 | SAM |
| 4 | 199 | 0.47 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 524 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4YNM · ASH1L wild-type SET domain in complex with S-adenosyl methionine (SAM) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9NR48
- Elsewhere: RCSB PDB 4YNM · PDBe 4YNM · UniProt Q9NR48
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