Research workbench
Crystal structure of H334R/Y306F HDAC8 in complex with a tetrapeptide substrate
Analyse Crystal structure of H334R/Y306F HDAC8 in complex with a tetrapeptide substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QA7
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8; Tetrapeptide substrate
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- ACE, MCM, K, ZN
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 365 | 40% helix, 13% strand | Q9BY41 |
| B | Tetrapeptide substrate | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- MCM · 7-amino-4-methyl-chromen-2-one · ligand · chains A, B
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.45 | 0.79 | 20 | GOL |
| 2 | 70 | 0.34 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, acetylation).
Compared structures
- 4QA7 · Crystal structure of H334R/Y306F HDAC8 in complex with a tetrapeptide substrate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BY41 · AlphaFold monomer V2.0 prediction for histone deacetylase 8 (Q9BY41) · 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 Q9BY41
- Elsewhere: RCSB PDB 4QA7 · PDBe 4QA7 · UniProt Q9BY41
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