Research workbench
Crystal structure of influenza a virus neuraminidase N5 complexed with zanamivir
Analyse Crystal structure of influenza a virus neuraminidase N5 complexed with zanamivir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SAN
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- A1ILL9
- Ligands
- ZMR, NAG, CA
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase (EC 3.2.1.18) | protein | 394 | 4% helix, 46% strand | A1ILL9 |
Ligands and binding sites
- ZMR · Zanamivir · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- CA · Calcium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.73 | 0.79 | 74 | GOL, ZMR |
| 2 | 266 | 0.62 | 0.81 | 43 | ZMR |
| 3 | 88 | 0.32 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 270 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3SAN · Crystal structure of influenza A virus neuraminidase N5 complexed with Zanamivir · 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
- Every structure of UniProt A1ILL9
- Elsewhere: RCSB PDB 3SAN · PDBe 3SAN · UniProt A1ILL9
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