Research workbench
Crystal structure of neuraminidase N6 complexed with laninamivir
Analyse Crystal structure of neuraminidase N6 complexed with laninamivir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QN6
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- Q2FCL6
- Ligands
- LNV, NAG, MAN, BMA, CA
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase | protein | 389 | 3% helix, 44% strand | Q2FCL6 |
Ligands and binding sites
- LNV · 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-D-glycero-D-galacto-non-2-enonic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- BMA · beta-D-mannopyranose · sugar · 4 copies
- CA · Calcium ion · metal · 2 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 | 278 | 0.65 | 0.82 | 46 | LNV |
| 2 | 290 | 0.64 | 0.81 | 45 | LNV |
| 3 | 275 | 0.53 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 80 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4QN6 · Crystal structure of Neuraminidase N6 complexed with Laninamivir · 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 Q2FCL6
- Elsewhere: RCSB PDB 4QN6 · PDBe 4QN6 · UniProt Q2FCL6
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