MolNFT v1 · #128717 · protein
Complex of I223V mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir
5NZ4: “Complex of I223V mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir”. X-ray diffraction, 5 ligands (G39, NAG, BMA), 4 pockets (best druggability 0.62). MolNFT v1 #128717 on GenesisL1: 3D structure, binding…
- PDB
- 5NZ4
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- C6KQL9
- Ligands
- G39, NAG, BMA, MAN, CA
- Pockets
- 4 · best druggability 0.62
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 | C6KQL9 |
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 · 9 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.62 | 0.81 | 42 | G39, EDO |
| 2 | 274 | 0.60 | 0.80 | 43 | G39 |
| 3 | 50 | 0.51 | 0.88 | 17 | EDO |
| 4 | 113 | 0.36 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 451 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5NZ4 · Complex of I223V 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 C6KQL9
- Elsewhere: RCSB PDB 5NZ4 · PDBe 5NZ4 · UniProt C6KQL9
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