MolNFT v1 · #128625 · protein
Complex of H275Y mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir
5NWE: “Complex of H275Y mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir”. X-ray diffraction, 6 ligands (G39, NAG, BMA), 17 pockets (best druggability 0.62). MolNFT v1 #128625 on GenesisL1: 3D structure, binding…
- PDB
- 5NWE
- Type
- protein
- Length
- 1,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- C9EKP8
- Ligands
- G39, NAG, BMA, MAN, FUC, CA
- Pockets
- 17 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 388 | 4% helix, 44% strand | C9EKP8 |
Ligands and binding sites
- G39 · (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy) cyclohex-1-ene-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, C, B, D
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.62 | 0.80 | 43 | G39 |
| 2 | 270 | 0.62 | 0.80 | 43 | G39 |
| 3 | 270 | 0.61 | 0.80 | 44 | G39 |
| 4 | 264 | 0.60 | 0.79 | 44 | G39 |
| 5 | 169 | 0.57 | 0.81 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1604 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1595 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1593 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1571 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5NWE · Complex of H275Y 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 C9EKP8
- Elsewhere: RCSB PDB 5NWE · PDBe 5NWE · UniProt C9EKP8
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