Research workbench
Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex
Analyse Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NCA
- 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
- P03472, P01865
- Ligands
- NAG, MAN, BMA, CA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Influenza a subtype N9 neuraminidase (EC 3.2.1.18) | protein | 389 | 4% helix, 43% strand | P03472 |
| L | IGG2A-kappa NC41 Fab (light chain) | protein | 214 | 6% helix, 50% strand | — |
| H | IGG2A-kappa NC41 Fab (heavy chain) | protein | 221 | 5% helix, 52% strand | P01865 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 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 | 601 | 0.75 | 0.82 | 63 | empty |
| 2 | 501 | 0.70 | 0.80 | 53 | empty |
| 3 | 163 | 0.43 | 0.74 | 18 | empty |
| 4 | 78 | 0.34 | 0.75 | 18 | empty |
| 5 | 64 | 0.29 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1909 Ų buried · 18 hydrogen bonds · protein-protein
- N–H · 604 Ų buried · 13 hydrogen bonds · protein-protein
- N–L · 522 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1NCA · 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 P03472
- Every structure of UniProt P01865
- Elsewhere: RCSB PDB 1NCA · PDBe 1NCA · UniProt P03472 · UniProt P01865
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