MolNFT v1 · #15686 · protein
Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex
1NCD · Influenza a subtype N9 neuraminidase: “Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 8 pockets (best druggability 0.75). MolNFT v1 #15686 on…
- PDB
- 1NCD
- Type
- protein
- Length
- 824 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Influenza a subtype N9 neuraminidase; IGG2A-kappa NC41 Fab (light chain); IGG2A-kappa…
- EC
- 3.2.1.18
- UniProt
- P05803, P01865
- Ligands
- NAG, MAN, BMA, CA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Influenza a subtype N9 neuraminidase (EC 3.2.1.18) | protein | 389 | 4% helix, 45% strand | P05803 |
| L | IGG2A-kappa NC41 Fab (light chain) | protein | 214 | 4% helix, 51% strand | — |
| H | IGG2A-kappa NC41 Fab (heavy chain) | protein | 221 | 7% helix, 53% strand | P01865 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains N
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.75 | 0.82 | 55 | empty |
| 2 | 381 | 0.67 | 0.80 | 36 | empty |
| 3 | 192 | 0.47 | 0.75 | 24 | empty |
| 4 | 152 | 0.39 | 0.73 | 32 | empty |
| 5 | 92 | 0.37 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1913 Ų buried · 16 hydrogen bonds · protein-protein
- N–H · 587 Ų buried · 10 hydrogen bonds · protein-protein
- N–L · 499 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1NCD · Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex · the same entry in another collection · chain N against N, TM-score 1.00
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.51
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 P05803
- Every structure of UniProt P01865
- Elsewhere: RCSB PDB 1NCD · PDBe 1NCD · UniProt P05803 · UniProt P01865
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