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Complex of I223V mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir
Analyse Complex of I223V mutant variant of neuraminidase from H1N1 influenza virus with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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