MolNFT v1 · #10565 · protein
Structures of aromatic inhibitors of influenza virus neuraminidase
1IVD · Influenza a subtype N2 neuraminidase: “Structures of aromatic inhibitors of influenza virus neuraminidase”. X-ray diffraction, 7 ligands (ST1, NAG, MAN), 5 pockets (best druggability 0.61). MolNFT v1 #10565 on GenesisL1: 3D…
- PDB
- 1IVD
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Influenza a subtype N2 neuraminidase
- EC
- 3.2.1.18
- UniProt
- P06820
- Ligands
- ST1, NAG, MAN, BMA, FUL, FUC, CA
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Influenza a subtype N2 neuraminidase (EC 3.2.1.18) | protein | 388 | 1% helix, 40% strand | P06820 |
Ligands and binding sites
- ST1 · 4-(acetylamino)-3-hydroxy-5-nitrobenzoic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies
- FUL · beta-L-fucopyranose · sugar · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains B
- 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.61 | 0.79 | 41 | ST1 |
| 2 | 313 | 0.60 | 0.78 | 42 | ST1 |
| 3 | 162 | 0.60 | 0.83 | 24 | empty |
| 4 | 202 | 0.52 | 0.78 | 32 | empty |
| 5 | 50 | 0.29 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1639 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 1IVD · Structures of aromatic inhibitors of influenza virus neuraminidase · 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 P06820
- Elsewhere: RCSB PDB 1IVD · PDBe 1IVD · UniProt P06820
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