MolNFT v1 · #111384 · protein
ASH1L set domain Q2265A mutant in complex with S-adenosyl methionine (SAM)
4YPA · Histone-lysine N-methyltransferase ASH1L: “ASH1L set domain Q2265A mutant in complex with S-adenosyl methionine (SAM)”. X-ray diffraction, 2 ligands (SAM, ZN), 11 pockets (best druggability 0.78). MolNFT v1 #111384 on GenesisL1: 3D…
- PDB
- 4YPA
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- 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
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase ASH1L (EC 2.1.1.43) | protein | 218 | 11% helix, 30% strand | Q9NR48 |
| B | Histone-lysine N-methyltransferase ASH1L (EC 2.1.1.43) | protein | 212 | 10% helix, 29% strand | Q9NR48 |
| C | Histone-lysine N-methyltransferase ASH1L (EC 2.1.1.43) | protein | 217 | 11% helix, 29% strand | Q9NR48 |
| D | Histone-lysine N-methyltransferase ASH1L (EC 2.1.1.43) | protein | 211 | 10% helix, 28% strand | Q9NR48 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.78 | 0.81 | 64 | empty |
| 2 | 957 | 0.77 | 0.80 | 82 | empty |
| 3 | 229 | 0.68 | 0.85 | 38 | SAM |
| 4 | 267 | 0.67 | 0.83 | 41 | SAM |
| 5 | 201 | 0.65 | 0.84 | 29 | SAM |
Interfaces
4 interfaces between chains.
- C–D · 708 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 695 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 371 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4YPA · ASH1L SET domain Q2265A mutant 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 4YPA · PDBe 4YPA · UniProt Q9NR48
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