Research workbench
Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from micromonospora viridifaciens.
Analyse Contribution of the active site aspartic acid to catalysis in the bacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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