Research workbench
Crystal structure of schistosoma mansoni HDAC8
Analyse Crystal structure of schistosoma mansoni HDAC8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BZ5
- Type
- protein
- Length
- 1,645 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- UniProt
- A5H660
- Ligands
- K, ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 | protein | 404 | 42% helix, 12% strand | A5H660 |
| B | Histone deacetylase 8 | protein | 419 | 42% helix, 12% strand | A5H660 |
| C | Histone deacetylase 8 | protein | 418 | 41% helix, 12% strand | A5H660 |
| D | Histone deacetylase 8 | protein | 404 | 42% helix, 12% strand | A5H660 |
Ligands and binding sites
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- TLA · L(+)-tartaric acid · 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 | 945 | 0.81 | 0.83 | 111 | TLA |
| 2 | 943 | 0.81 | 0.83 | 102 | TLA |
| 3 | 320 | 0.56 | 0.76 | 42 | empty |
| 4 | 243 | 0.55 | 0.78 | 33 | empty |
| 5 | 97 | 0.46 | 0.80 | 23 | TLA |
Interfaces
4 interfaces between chains.
- A–B · 1255 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1248 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 298 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 277 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4BZ5 · Crystal structure of Schistosoma mansoni HDAC8 · 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 4BZ5 · PDBe 4BZ5 · UniProt A5H660
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