MolNFT v1 · #128726 · protein
Complex of S247N mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir
5NZE: “Complex of S247N mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir”. X-ray diffraction, 5 ligands (G39, NAG, BMA), 5 pockets (best druggability 0.64). MolNFT v1 #128726 on GenesisL1: 3D structure, binding…
- PDB
- 5NZE
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- W5R8B8
- Ligands
- G39, NAG, BMA, MAN, CA
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase | protein | 387 | 3% helix, 45% strand | W5R8B8 |
Ligands and binding sites
- G39 · (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy) cyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 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 | 275 | 0.64 | 0.81 | 44 | G39 |
| 2 | 296 | 0.63 | 0.81 | 43 | G39 |
| 3 | 50 | 0.52 | 0.88 | 17 | empty |
| 4 | 50 | 0.51 | 0.88 | 17 | EDO |
| 5 | 113 | 0.38 | 0.74 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 450 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5NZE · Complex of S247N mutant variant of neuraminidase from H1N1 influenza virus with… · 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 W5R8B8
- Elsewhere: RCSB PDB 5NZE · PDBe 5NZE · UniProt W5R8B8
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