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Crystal structure of Schistosoma mansoni HDAC8 H292M mutant complexed with NCC-149
Analyse Crystal structure of Schistosoma mansoni HDAC8 H292M mutant complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HSG
- Type
- protein
- Length
- 1,622 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.846
- Source
- Schistosoma mansoni
- Molecule
- Histone deacetylase
- EC
- 3.5.1.98
- UniProt
- A5H660
- Ligands
- GM5, K, ZN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.846 · 4 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase (EC 3.5.1.98) | protein | 400 | 42% helix, 13% strand | A5H660 |
| B | Histone deacetylase (EC 3.5.1.98) | protein | 412 | 42% helix, 13% strand | A5H660 |
| C | Histone deacetylase (EC 3.5.1.98) | protein | 412 | 43% helix, 13% strand | A5H660 |
| D | Histone deacetylase (EC 3.5.1.98) | protein | 398 | 42% helix, 13% strand | A5H660 |
Ligands and binding sites
- GM5 · ~{N}-oxidanyl-3-[1-(phenylsulfanylmethyl)-1,2,3-triazol-4-yl]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 · 17 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.81 | 0.82 | 111 | DMF, ZN, GM5, GOL |
| 2 | 1041 | 0.81 | 0.82 | 105 | ZN, GM5, GOL |
| 3 | 441 | 0.63 | 0.77 | 47 | DMF |
| 4 | 339 | 0.58 | 0.76 | 39 | DMF |
| 5 | 173 | 0.44 | 0.74 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1031 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1014 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 333 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 301 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6HSG · Crystal structure of schistosoma mansoni HDAC8 H292M mutant complexed with ncc-149 · 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 6HSG · PDBe 6HSG · UniProt A5H660
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