Research workbench
N2 neuraminidase in complex with a novel antiviral compound
Analyse N2 neuraminidase in complex with a novel antiviral compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BR6
- Type
- protein
- Length
- 387 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- C6KNH8
- Ligands
- E3M, NAG, MAN, BMA, NI, CA
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuraminidase (EC 3.2.1.18) | protein | 387 | 3% helix, 48% strand | C6KNH8 |
Ligands and binding sites
- E3M · (1R)-4-acetamido-3-amino-1,5-anhydro-2,3,4-trideoxy-1-sulfo-D-glycero-D-galacto-octitol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar
- NI · Nickel (II) ion · metal · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.60 | 0.79 | 44 | GOL, E3M |
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6BR6 · N2 neuraminidase in complex with a novel antiviral compound · 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 C6KNH8
- Elsewhere: RCSB PDB 6BR6 · PDBe 6BR6 · UniProt C6KNH8
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