Research workbench
Crystal structure of P91L-Y306F HDAC8 in complex with a tetrapeptide substrate
Analyse Crystal structure of P91L-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
- 5D1D
- Type
- protein
- Length
- 732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8; HDAC8 fluor de lys tetrapeptide substrate
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- ACE, MCM, K, ZN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 364 | 40% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 360 | 41% helix, 13% strand | Q9BY41 |
| C, D | HDAC8 fluor de lys tetrapeptide substrate | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.79 | 0.81 | 90 | MCM |
| 2 | 499 | 0.68 | 0.79 | 51 | empty |
| 3 | 67 | 0.67 | 0.94 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 868 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 456 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 426 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 163 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, acetylation).
Compared structures
- 5D1D · Crystal structure of P91L-Y306F HDAC8 in complex with a tetrapeptide substrate · 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 Q9BY41
- Elsewhere: RCSB PDB 5D1D · PDBe 5D1D · UniProt Q9BY41
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