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The crystal structure of neuramindase from A/canine/IL/11613/2015 (H3N2) influenza virus.
Analyse The crystal structure of neuramindase from A/canine/IL/11613/2015 (H3N2)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N4D
- Type
- protein
- Length
- 1,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- unidentified influenza virus
- Molecule
- Neuraminidase
- UniProt
- A0A0H3YBU9
- Ligands
- NAG, MAN, BMA, CA
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase | protein | 388 | 3% helix, 49% strand | A0A0H3YBU9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, D, B, C
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains B, D, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.62 | 0.80 | 46 | empty |
| 2 | 269 | 0.60 | 0.80 | 41 | empty |
| 3 | 297 | 0.60 | 0.78 | 42 | empty |
| 4 | 206 | 0.60 | 0.81 | 26 | empty |
| 5 | 272 | 0.60 | 0.79 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1649 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1648 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6N4D · The crystal structure of neuramindase from A/CANINE/IL/11613/2015 (H3N2) influenza virus. · 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 A0A0H3YBU9
- Elsewhere: RCSB PDB 6N4D · PDBe 6N4D · UniProt A0A0H3YBU9
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