Research workbench
Crystal structure of Schistosoma mansoni HDAC8 complexed with an hydroxamate 3
Analyse Crystal structure of Schistosoma mansoni HDAC8 complexed with an hydroxamate 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GXU
- Type
- protein
- Length
- 1,609 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.917
- Source
- Schistosoma mansoni
- Molecule
- Histone deacetylase
- EC
- 3.5.1.98
- UniProt
- A5H660
- Ligands
- FG8, K, ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.917 · 4 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase (EC 3.5.1.98) | protein | 391 | 42% helix, 13% strand | A5H660 |
| B | Histone deacetylase (EC 3.5.1.98) | protein | 410 | 42% helix, 12% strand | A5H660 |
| C | Histone deacetylase (EC 3.5.1.98) | protein | 411 | 43% helix, 12% strand | A5H660 |
| D | Histone deacetylase (EC 3.5.1.98) | protein | 397 | 44% helix, 13% strand | A5H660 |
Ligands and binding sites
- FG8 · (~{E})-3-[2-(4-chlorophenyl)sulfanylphenyl]-~{N}-oxidanyl-prop-2-enamide · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- DMF · Dimethylformamide · additive · 25 copies · chains A, B, D, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.81 | 0.82 | 105 | FG8, DMF, GOL |
| 2 | 1034 | 0.81 | 0.82 | 112 | ZN, FG8, DMF, GOL |
| 3 | 364 | 0.62 | 0.78 | 44 | DMF |
| 4 | 249 | 0.59 | 0.79 | 35 | DMF |
| 5 | 202 | 0.48 | 0.75 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 987 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 983 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 352 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6GXU · Crystal structure of schistosoma mansoni HDAC8 complexed with an hydroxamate 3 · 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 A5H660
- Elsewhere: RCSB PDB 6GXU · PDBe 6GXU · UniProt A5H660
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