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
- 2AEQ
- Type
- protein
- Length
- 611 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; Fab light chain; Fab heavy chain
- EC
- 3.2.1.-
- UniProt
- Q80DL0
- Ligands
- NAG, MAN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuraminidase (EC 3.2.1.-) | protein | 388 | 3% helix, 47% strand | Q80DL0 |
| L | Fab light chain | protein | 107 | 3% helix, 48% strand | — |
| H | Fab heavy chain | protein | 116 | 0% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, L
- MAN · alpha-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.72 | 0.80 | 73 | empty |
| 2 | 99 | 0.37 | 0.75 | 18 | empty |
| 3 | 62 | 0.31 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 781 Ų buried · 2 hydrogen bonds · protein-protein
- A–H · 589 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 381 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 2AEQ · 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
- Every structure of UniProt Q80DL0
- Elsewhere: RCSB PDB 2AEQ · PDBe 2AEQ · UniProt Q80DL0
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