Research workbench
Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium PG7 in complex with N-acetyl-2,3-dehydro-2- deoxyneuraminic acid
Analyse Crystal structure of an inverting family GH156 exosialidase from uncultured… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S0E
- Type
- protein
- Length
- 992 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosialidase from uncultured bacterium PG7
- EC
- 3.2.1.18
- Ligands
- DAN
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exosialidase from uncultured bacterium PG7 (EC 3.2.1.18) | protein | 496 | 30% helix, 22% strand | — |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.86 | 0.89 | 80 | TRS, GOL |
| 2 | 426 | 0.69 | 0.81 | 38 | empty |
| 3 | 392 | 0.68 | 0.81 | 40 | GOL |
| 4 | 290 | 0.62 | 0.80 | 30 | TRS |
| 5 | 162 | 0.53 | 0.79 | 24 | GOL, PG4, DAN |
Interfaces
1 interface between chains.
- A–B · 1839 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6S0E · Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7… · 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
- Elsewhere: RCSB PDB 6S0E · PDBe 6S0E
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