Research workbench
An epidemiologically significant epitope of a 1998 influenza virus neuraminidase forms a highly hydrated interface in the na-antibody complex.
Analyse An epidemiologically significant epitope of a 1998 influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AEP
- Type
- protein
- Length
- 660 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; Fab heavy chain; Fab light chain
- EC
- 3.2.1.18
- Ligands
- NAG, MAN, GLC, BMA, CA, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuraminidase (EC 3.2.1.18) | protein | 388 | 3% helix, 47% strand | — |
| H | Fab heavy chain | protein | 143 | 8% helix, 44% strand | — |
| L | Fab light chain | protein | 129 | 2% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, L
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains L
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, H, L
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.70 | 0.79 | 54 | SO4 |
| 2 | 572 | 0.65 | 0.76 | 55 | empty |
| 3 | 133 | 0.41 | 0.74 | 30 | GLC |
| 4 | 72 | 0.34 | 0.76 | 16 | empty |
| 5 | 66 | 0.29 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1024 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 651 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 442 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 2AEP · An epidemiologically significant epitope of a 1998 influenza virus neuraminidase forms a… · 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
- Elsewhere: RCSB PDB 2AEP · PDBe 2AEP
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