MolNFT v1 · #25889 · protein
Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from micromonospora viridifaciens
1W8O · Bacterial sialidase: “Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from micromonospora…”. X-ray diffraction, 3 ligands (GLC, GAL, NA), 5 pockets (best druggability 0.72). MolNFT v1 #25889…
- PDB
- 1W8O
- Type
- protein
- Length
- 601 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial sialidase
- EC
- 3.2.1.18
- UniProt
- Q02834
- Ligands
- GLC, GAL, NA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacterial sialidase (EC 3.2.1.18) | protein | 601 | 3% helix, 48% strand | Q02834 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar
- GAL · beta-D-galactopyranose · sugar · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.72 | 0.88 | 36 | empty |
| 2 | 134 | 0.42 | 0.75 | 18 | CIT, GOL |
| 3 | 103 | 0.38 | 0.76 | 23 | empty |
| 4 | 137 | 0.38 | 0.73 | 21 | empty |
| 5 | 73 | 0.34 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1W8O · Contribution of the Active Site Aspartic Acid to Catalysis in the Bacterial Neuraminidase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02834 · AlphaFold monomer V2.0 prediction for sialidase (Q02834) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q02834
- Elsewhere: RCSB PDB 1W8O · PDBe 1W8O · UniProt Q02834
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