Research workbench
Crystal structure of H142A-Y306F HDAC8 in complex with a tetrapeptide substrate
Analyse Crystal structure of H142A-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
- 5DC8
- Type
- protein
- Length
- 734 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8; Fluor-de-lys tetrapeptide assay substrate
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- ACE, MCM, K, ZN
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 363 | 40% helix, 13% strand | Q9BY41 |
| C, D | Fluor-de-lys tetrapeptide assay substrate | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, D
- MCM · 7-amino-4-methyl-chromen-2-one · ligand · 2 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.81 | 0.82 | 102 | MCM |
| 2 | 519 | 0.74 | 0.83 | 58 | GOL |
Interfaces
5 interfaces between chains.
- A–B · 1090 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 467 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 462 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 168 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 123 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, acetylation).
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 5DC8 · PDBe 5DC8 · UniProt Q9BY41
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