Research workbench
Influenza a virus N6 neuraminidase complex with dana (DUCK/ENGLAND/56).
Analyse Influenza a virus N6 neuraminidase complex with dana (DUCK/ENGLAND/56). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HFY
- 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
- DAN, NAG, MAN, BMA, CA
- Pockets
- 15 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 389 | 3% helix, 44% strand | Q6XV27 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains C, A, D, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, A, D, B
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.63 | 0.81 | 47 | DAN |
| 2 | 379 | 0.62 | 0.78 | 53 | empty |
| 3 | 265 | 0.62 | 0.80 | 38 | DAN |
| 4 | 262 | 0.61 | 0.80 | 39 | DAN |
| 5 | 287 | 0.60 | 0.79 | 40 | DAN |
Interfaces
6 interfaces between chains.
- C–D · 1763 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1756 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1730 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1728 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 6HFY · Influenza A virus N6 neuraminidase complex with DANA (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 6HFY · PDBe 6HFY · UniProt Q6XV27
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