MolNFT v1 · #137228 · protein
Crystal structure of histone deacetylase 8 in complex with trapoxin a
5VI6: “Crystal structure of histone deacetylase 8 in complex with trapoxin a”. X-ray diffraction, 3 ligands (5OM, K, ZN), 1 pocket (best druggability 0.49). MolNFT v1 #137228 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VI6
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8; Trapoxin a
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- 5OM, K, ZN
- Pockets
- 1 · best druggability 0.49
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 | 353 | 41% helix, 13% strand | Q9BY41 |
| B | Trapoxin a | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 5OM · (2S)-2-amino-8,8-dihydroxy-8-[(2S)-oxiran-2-yl]octanoic acid · ligand · chains A, B
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.49 | 0.84 | 23 | 5OM, EDO |
Interfaces
1 interface between chains.
- A–B · 187 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 5VI6 · Crystal structure of histone deacetylase 8 in complex with trapoxin A · 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 5VI6 · PDBe 5VI6 · UniProt Q9BY41
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