MolNFT v1 · #151195 · protein
Influenza a virus N6 neuraminidase native structure (DUCK/ENGLAND/56).
6HGB: “Influenza a virus N6 neuraminidase native structure (DUCK/ENGLAND/56).”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 17 pockets (best druggability 0.63). MolNFT v1 #151195 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6HGB
- Type
- protein
- Length
- 1,556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- Q6XV27
- Ligands
- NAG, MAN, BMA, CA, PO4
- Pockets
- 17 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 389 | 3% helix, 43% strand | Q6XV27 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains C, A, D, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, A, D, B
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, B
- GOL · Glycerol · additive · 25 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 19 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.63 | 0.81 | 41 | GOL |
| 2 | 273 | 0.62 | 0.80 | 45 | PEG |
| 3 | 306 | 0.62 | 0.80 | 41 | GOL |
| 4 | 267 | 0.61 | 0.80 | 35 | GOL |
| 5 | 280 | 0.61 | 0.80 | 42 | GOL |
Interfaces
6 interfaces between chains.
- A–C · 1762 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1760 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1729 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1727 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6HGB · Influenza A virus N6 neuraminidase native structure (Duck/England/56). · 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 Q6XV27
- Elsewhere: RCSB PDB 6HGB · PDBe 6HGB · UniProt Q6XV27
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