Research workbench
Crystal structure of schistosoma mansoni HDAC8 complexed with J1038
Analyse Crystal structure of schistosoma mansoni HDAC8 complexed with J1038 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BZ8
- Type
- protein
- Length
- 1,615 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- UniProt
- A5H660
- Ligands
- J38, K, ZN
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 | protein | 393 | 42% helix, 13% strand | A5H660 |
| B | Histone deacetylase 8 | protein | 415 | 41% helix, 12% strand | A5H660 |
| C | Histone deacetylase 8 | protein | 413 | 42% helix, 13% strand | A5H660 |
| D | Histone deacetylase 8 | protein | 394 | 42% helix, 13% strand | A5H660 |
Ligands and binding sites
- J38 · (2R)-2-methyl-3-oxo-4H-1,4-benzothiazine-6-carbohydroxamic acid · 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
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 | 1113 | 0.80 | 0.82 | 107 | J38 |
| 2 | 1056 | 0.80 | 0.81 | 109 | J38 |
| 3 | 357 | 0.66 | 0.80 | 43 | empty |
| 4 | 242 | 0.57 | 0.78 | 26 | empty |
| 5 | 50 | 0.43 | 0.83 | 19 | J38 |
Interfaces
4 interfaces between chains.
- C–D · 1074 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 997 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 342 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 305 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4BZ8 · Crystal structure of Schistosoma mansoni HDAC8 complexed with J1038 · 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 4BZ8 · PDBe 4BZ8 · UniProt A5H660
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