MolNFT v1 · #16016 · protein
The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping binding site of the NC41 antibody
1NMB · N9 neuraminidase: “The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with…”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 5 pockets (best druggability 0.67). MolNFT v1 #16016 on…
- PDB
- 1NMB
- Type
- protein
- Length
- 619 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, CA
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | N9 neuraminidase (EC 3.2.1.18) | protein | 388 | 3% helix, 41% strand | P05803 |
| L | Fab NC10 | protein | 109 | 3% helix, 48% strand | — |
| H | Fab NC10 | protein | 122 | 7% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains N
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains N, H, L
- BMA · beta-D-mannopyranose · sugar · chains N
- CA · Calcium ion · metal · chains N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.67 | 0.78 | 68 | empty |
| 2 | 97 | 0.38 | 0.76 | 15 | MAN |
| 3 | 81 | 0.32 | 0.74 | 19 | empty |
| 4 | 73 | 0.31 | 0.74 | 17 | empty |
| 5 | 56 | 0.29 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- L–H · 755 Ų buried · 10 hydrogen bonds · protein-protein
- N–H · 406 Ų buried · 5 hydrogen bonds · protein-protein
- N–L · 392 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1NMB · The structure of a complex between the NC10 antibody and influenza virus neuraminidase… · 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 1NMB · PDBe 1NMB · UniProt P05803
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