MolNFT v1 · #116390 · protein
Crystal structure of D176N-Y306F HDAC8 in complex with a tetrapeptide substrate
5DC6 · Histone deacetylase 8: “Crystal structure of D176N-Y306F HDAC8 in complex with a tetrapeptide substrate”. X-ray diffraction, 4 ligands (ACE, MCM, ZN), 3 pockets (best druggability 0.80). MolNFT v1 #116390 on GenesisL1: 3D structure…
- PDB
- 5DC6
- Type
- protein
- Length
- 735 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, ZN, K
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 363 | 40% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 364 | 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
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- K · Potassium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 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 | 1034 | 0.80 | 0.82 | 99 | MCM, GOL |
| 2 | 476 | 0.72 | 0.82 | 56 | GOL |
| 3 | 109 | 0.61 | 0.87 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1014 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 471 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 466 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 167 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 162 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, acetylation).
Compared structures
- 5DC6 · Crystal structure of D176N-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 5DC6 · PDBe 5DC6 · UniProt Q9BY41
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