MolNFT v1 · #116031 · protein
Crystal structure of G117E HDAC8 in complex with tsa
5D1B · Histone deacetylase 8: “Crystal structure of G117E HDAC8 in complex with tsa”. X-ray diffraction, 3 ligands (TSN, K, ZN), 6 pockets (best druggability 0.78). MolNFT v1 #116031 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5D1B
- Type
- protein
- Length
- 721 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- TSN, K, ZN
- Pockets
- 6 · best druggability 0.78
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 | 356 | 40% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 365 | 40% helix, 12% strand | Q9BY41 |
Ligands and binding sites
- TSN · Trichostatin A · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.78 | 0.80 | 89 | ZN, TSN |
| 2 | 61 | 0.64 | 0.94 | 20 | empty |
| 3 | 91 | 0.61 | 0.88 | 21 | empty |
| 4 | 65 | 0.34 | 0.76 | 17 | empty |
| 5 | 52 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 688 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5D1B · Crystal structure of G117E HDAC8 in complex with TSA · 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 5D1B · PDBe 5D1B · UniProt Q9BY41
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