Research workbench
Crystal structure of MYST acetyltransferase domain in complex with inhibitor 40
Analyse Crystal structure of MYST acetyltransferase domain in complex with inhibitor 40 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PDE
- Type
- protein
- Length
- 268 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.22
- Source
- Homo sapiens
- Molecule
- Histone acetyltransferase KAT8
- EC
- 2.3.1.48
- UniProt
- Q9H7Z6
- Ligands
- O9V, ZN, NA, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.22 · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase KAT8 (EC 2.3.1.48) | protein | 268 | 36% helix, 24% strand | Q9H7Z6 |
Ligands and binding sites
- O9V · 2-fluoro-3-methyl-N'-(phenylsulfonyl)-5-propoxybenzohydrazide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.66 | 0.82 | 40 | GOL, O9V |
| 2 | 75 | 0.51 | 0.84 | 17 | empty |
| 3 | 53 | 0.41 | 0.82 | 15 | empty |
| 4 | 75 | 0.34 | 0.75 | 14 | empty |
| 5 | 70 | 0.33 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 6PDE · Crystal structure of myst acetyltransferase domain in complex with inhibitor 40 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H7Z6 · AlphaFold monomer V2.0 prediction for histone acetyltransferase KAT8 (Q9H7Z6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9H7Z6
- Elsewhere: RCSB PDB 6PDE · PDBe 6PDE · UniProt Q9H7Z6
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