Research workbench
Crystal structure of schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 11
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
- 6HU2
- Type
- protein
- Length
- 1,632 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
- T34, K, ZN
- Pockets
- 13 · 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 (EC 3.5.1.98) | protein | 401 | 42% helix, 12% strand | A5H660 |
| B | Histone deacetylase (EC 3.5.1.98) | protein | 414 | 42% helix, 13% strand | A5H660 |
| C | Histone deacetylase (EC 3.5.1.98) | protein | 414 | 43% helix, 12% strand | A5H660 |
| D | Histone deacetylase (EC 3.5.1.98) | protein | 403 | 43% helix, 12% strand | A5H660 |
Ligands and binding sites
- T34 · 4-methyl-~{N}-oxidanyl-3-[(phenylmethyl)amino]benzamide · 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 · 19 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.81 | 0.82 | 105 | ZN, T34, DMF, GOL |
| 2 | 1030 | 0.80 | 0.81 | 113 | ZN, T34, DMF, GOL |
| 3 | 481 | 0.62 | 0.75 | 45 | empty |
| 4 | 275 | 0.59 | 0.79 | 28 | empty |
| 5 | 257 | 0.49 | 0.74 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1049 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 947 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 365 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 353 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HU2 · 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 6HU2 · PDBe 6HU2 · UniProt A5H660
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