Research workbench
Crystal structure of schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 12
Analyse Crystal structure of schistosoma mansoni HDAC8 complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P3S
- Type
- protein
- Length
- 1,620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase
- UniProt
- A5H660
- Ligands
- 5IB, K, ZN
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase | protein | 399 | 43% helix, 13% strand | A5H660 |
| B | Histone deacetylase | protein | 409 | 42% helix, 12% strand | A5H660 |
| C | Histone deacetylase | protein | 412 | 42% helix, 12% strand | A5H660 |
| D | Histone deacetylase | protein | 400 | 43% helix, 13% strand | A5H660 |
Ligands and binding sites
- 5IB · ~{N}-[2-methoxy-5-(oxidanylcarbamoyl) phenyl]dibenzofuran-4-carboxamide · 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
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.80 | 0.82 | 108 | 5IB, ZN, GOL |
| 2 | 1100 | 0.78 | 0.80 | 97 | GOL |
| 3 | 362 | 0.60 | 0.77 | 34 | empty |
| 4 | 307 | 0.58 | 0.77 | 35 | empty |
| 5 | 132 | 0.52 | 0.81 | 24 | 5IB |
Interfaces
4 interfaces between chains.
- A–B · 985 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 957 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 384 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 345 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7P3S · Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate… · 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 7P3S · PDBe 7P3S · UniProt A5H660
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.