Research workbench
Crystal structure of schistosoma mansoni HDAC8 complexed with J1075
Analyse Crystal structure of schistosoma mansoni HDAC8 complexed with J1075 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BZ9
- Type
- protein
- Length
- 1,621 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- UniProt
- A5H660
- Ligands
- KMY, K, ZN
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 | protein | 396 | 42% helix, 13% strand | A5H660 |
| B | Histone deacetylase 8 | protein | 414 | 43% helix, 12% strand | A5H660 |
| C | Histone deacetylase 8 | protein | 413 | 42% helix, 12% strand | A5H660 |
| D | Histone deacetylase 8 | protein | 398 | 43% helix, 13% strand | A5H660 |
Ligands and binding sites
- KMY · 3-chlorobenzothiophene-2-carbohydroxamic acid · ligand · 8 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 · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.81 | 0.82 | 110 | DMF, KMY, GOL |
| 2 | 917 | 0.79 | 0.81 | 95 | empty |
| 3 | 359 | 0.65 | 0.79 | 38 | empty |
| 4 | 112 | 0.62 | 0.87 | 23 | KMY |
| 5 | 282 | 0.59 | 0.78 | 34 | DMF |
Interfaces
4 interfaces between chains.
- C–D · 1029 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 477 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 347 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4BZ9 · Crystal structure of Schistosoma mansoni HDAC8 complexed with J1075 · 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 4BZ9 · PDBe 4BZ9 · UniProt A5H660
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