Research workbench
Crystal structures of two mutant neuraminidase-antibody complexes with amino acid substitutions in the interface
Analyse Crystal structures of two mutant neuraminidase-antibody complexes with amino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NCB
- 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
- 7 · best druggability 0.73
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 | P03472 |
| L | IGG2A-kappa NC41 Fab (light chain) | protein | 214 | 6% helix, 53% strand | — |
| H | IGG2A-kappa NC41 Fab (heavy chain) | protein | 221 | 8% helix, 51% 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.73 | 0.81 | 57 | empty |
| 2 | 547 | 0.68 | 0.78 | 49 | empty |
| 3 | 218 | 0.49 | 0.75 | 21 | empty |
| 4 | 157 | 0.39 | 0.72 | 26 | empty |
| 5 | 78 | 0.36 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1938 Ų buried · 15 hydrogen bonds · protein-protein
- N–H · 568 Ų buried · 11 hydrogen bonds · protein-protein
- N–L · 491 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1NCB · Crystal structures of two mutant neuraminidase-antibody complexes with amino acid… · 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 1NCB · PDBe 1NCB · UniProt P03472 · UniProt P01865
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