Research workbench
N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 4 FNI9 Fab molecules
Analyse N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 4 FNI9 Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8G3N
- Type
- protein
- Length
- 2,512 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens; Influenza A virus
- Molecule
- Neuraminidase; FNI9 Fab heavy chain; FNI9 Fab light chain
- UniProt
- V9SU56
- Ligands
- NAG, MAN, BMA, FUC, CA
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · resolution 2.9 · 3 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, J, K, L | Neuraminidase | protein | 388 | 2% helix, 48% strand | V9SU56 |
| E, A, B, C | FNI9 Fab heavy chain | protein | 130 | 5% helix, 46% strand | — |
| F, D, H, I | FNI9 Fab light chain | protein | 110 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 46 copies · chains G, J, K, L, H, I
- MAN · alpha-D-mannopyranose · sugar · 20 copies · chains J, K, L, G
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains J, K, L, G
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains J, L
- CA · Calcium ion · metal · 5 copies · chains G, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.74 | 0.83 | 63 | empty |
| 2 | 494 | 0.73 | 0.82 | 61 | empty |
| 3 | 481 | 0.73 | 0.82 | 57 | empty |
| 4 | 465 | 0.73 | 0.82 | 54 | empty |
| 5 | 412 | 0.70 | 0.81 | 41 | CA |
Interfaces
16 interfaces between chains.
- K–L · 1668 Ų buried · 27 hydrogen bonds · protein-protein
- G–J · 1665 Ų buried · 27 hydrogen bonds · protein-protein
- G–L · 1664 Ų buried · 27 hydrogen bonds · protein-protein
- J–K · 1664 Ų buried · 27 hydrogen bonds · protein-protein
- L–C · 917 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 23 glycan (disulfide, N-glycosylation).
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 V9SU56
- Elsewhere: RCSB PDB 8G3N · PDBe 8G3N · UniProt V9SU56
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