MolNFT v1 · #116032 · protein
Crystal structure of D233G-Y306F HDAC8 in complex with a tetrapeptide substrate
5D1C · Histone deacetylase 8: “Crystal structure of D233G-Y306F HDAC8 in complex with a tetrapeptide substrate”. X-ray diffraction, 4 ligands (ACE, MCM, K), 3 pockets (best druggability 0.86). MolNFT v1 #116032 on GenesisL1: 3D structure…
- PDB
- 5D1C
- Type
- protein
- Length
- 736 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 0.86
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 | 364 | 40% 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, B, 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 · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.86 | 0.89 | 98 | MCM |
| 2 | 369 | 0.73 | 0.85 | 49 | GOL |
| 3 | 200 | 0.47 | 0.75 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 945 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 460 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 170 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 118 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 5D1C · PDBe 5D1C · UniProt Q9BY41
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