Research workbench
Crystal structure of schistosoma mansoni HDAC8 complexed with an hydroxamate 2
Analyse Crystal structure of schistosoma mansoni HDAC8 complexed with an hydroxamate 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GXA
- Type
- protein
- Length
- 1,626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase
- EC
- 3.5.1.98
- UniProt
- A5H660
- Ligands
- TB8, K, ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase (EC 3.5.1.98) | protein | 399 | 42% helix, 13% strand | A5H660 |
| B | Histone deacetylase (EC 3.5.1.98) | protein | 416 | 42% helix, 13% strand | A5H660 |
| C | Histone deacetylase (EC 3.5.1.98) | protein | 412 | 42% helix, 13% strand | A5H660 |
| D | Histone deacetylase (EC 3.5.1.98) | protein | 399 | 43% helix, 13% strand | A5H660 |
Ligands and binding sites
- TB8 · (~{E})-3-(2-chlorophenyl)-~{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 · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, C
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 | 1009 | 0.81 | 0.82 | 106 | TB8, GOL |
| 2 | 917 | 0.81 | 0.83 | 93 | TB8, GOL |
| 3 | 362 | 0.64 | 0.79 | 44 | empty |
| 4 | 340 | 0.61 | 0.78 | 45 | DMF |
| 5 | 192 | 0.44 | 0.73 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1087 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1012 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 340 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6GXA · Crystal structure of Schistosoma mansoni HDAC8 complexed with an hydroxamate 2 · 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 6GXA · PDBe 6GXA · UniProt A5H660
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