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N9 neuraminidase complexes with antibodies NC41 and NC10: empirical free-energy calculations capture specificity trends observed with mutant binding data
Analyse N9 neuraminidase complexes with antibodies NC41 and NC10: empirical free-energy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NMA
- Type
- protein
- Length
- 609 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N9 neuraminidase; Fab NC10
- EC
- 3.2.1.18
- UniProt
- P05803
- Ligands
- NAG, MAN, BMA
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | N9 neuraminidase (EC 3.2.1.18) | protein | 378 | 2% helix, 47% strand | P05803 |
| L | Fab NC10 | protein | 109 | 3% helix, 45% strand | — |
| H | Fab NC10 | protein | 122 | 10% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains N
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains N, H
- BMA · beta-D-mannopyranose · sugar · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.65 | 0.77 | 57 | empty |
| 2 | 109 | 0.42 | 0.77 | 17 | empty |
| 3 | 112 | 0.40 | 0.76 | 21 | MAN |
| 4 | 90 | 0.37 | 0.76 | 17 | empty |
| 5 | 57 | 0.37 | 0.79 | 9 | empty |
Interfaces
3 interfaces between chains.
- L–H · 773 Ų buried · 9 hydrogen bonds · protein-protein
- N–H · 422 Ų buried · 6 hydrogen bonds · protein-protein
- N–L · 417 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1NMA · N9 neuraminidase complexes with antibodies NC41 and NC10: empirical free-energy… · the same entry in another collection · chain N against N, 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 P05803
- Elsewhere: RCSB PDB 1NMA · PDBe 1NMA · UniProt P05803
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