MolNFT v1 · #25888 · protein
Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from micromonospora viridifaciens.
1W8N · Bacterial sialidase: “Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from micromonospora…”. X-ray diffraction, 3 ligands (DAN, GAL, NA), 5 pockets (best druggability 0.73). MolNFT v1 #25888…
- PDB
- 1W8N
- 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
- DAN, GAL, NA
- Pockets
- 5 · best druggability 0.73
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
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- NA · Sodium ion · metal · 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 | 208 | 0.73 | 0.89 | 32 | empty |
| 2 | 120 | 0.40 | 0.75 | 19 | DAN |
| 3 | 162 | 0.39 | 0.73 | 26 | empty |
| 4 | 73 | 0.33 | 0.75 | 14 | empty |
| 5 | 54 | 0.30 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1W8N · 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 0.96
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 1W8N · PDBe 1W8N · UniProt Q02834
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