MolNFT v1 · #163341 · protein
Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium PG7 in complex with N-glycolylneuraminic acid
6S04: “Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium PG7 in complex with…”. X-ray diffraction, 1 ligand (NGE), 3 pockets (best druggability 0.86). MolNFT v1 #163341 on GenesisL1: 3D structure…
- PDB
- 6S04
- 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
- NGE
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosialidase from uncultured bacterium PG7 (EC 3.2.1.18) | protein | 495 | 30% helix, 22% strand | — |
| B | Exosialidase from uncultured bacterium PG7 (EC 3.2.1.18) | protein | 497 | 30% helix, 22% strand | — |
Ligands and binding sites
- NGE · N-glycolyl-beta-neuraminic acid · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.86 | 0.87 | 110 | ACT |
| 2 | 733 | 0.72 | 0.78 | 64 | GOL, NGE |
| 3 | 186 | 0.52 | 0.77 | 26 | ACT, NGE |
Interfaces
1 interface between chains.
- A–B · 1819 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 6S04 · 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 6S04 · PDBe 6S04
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