Research workbench
Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium PG7 in complex with N-acetylneuraminic 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
- 6S00
- Type
- protein
- Length
- 991 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
- SLB
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosialidase from uncultured bacterium PG7 (EC 3.2.1.18) | protein | 495 | 31% helix, 22% strand | — |
| B | Exosialidase from uncultured bacterium PG7 (EC 3.2.1.18) | protein | 496 | 31% helix, 22% strand | — |
Ligands and binding sites
- SLB · N-acetyl-beta-neuraminic acid · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 11 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.87 | 0.88 | 123 | GOL |
| 2 | 329 | 0.64 | 0.80 | 37 | empty |
| 3 | 166 | 0.55 | 0.80 | 25 | GOL, SLB |
| 4 | 133 | 0.53 | 0.81 | 23 | GOL, SLB |
Interfaces
1 interface between chains.
- A–B · 1815 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6S00 · 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 6S00 · PDBe 6S00
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