MolNFT v1 · #157655 · protein
The complex crystal structure of neuraminidase from A/MINNESOTA/11/2010 with B10 antibody.
6N6B: “The complex crystal structure of neuraminidase from A/MINNESOTA/11/2010 with B10 antibody.”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 6 pockets (best druggability 0.82). MolNFT v1 #157655 on GenesisL1: 3D structure, binding…
- PDB
- 6N6B
- Type
- protein
- Length
- 823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; B10 antibody heavy chain Fab; B10 antibody light chain Fab
- EC
- 3.2.1.18
- UniProt
- A0A075ETL7
- Ligands
- NAG, MAN, BMA, CA
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuraminidase (EC 3.2.1.18) | protein | 388 | 3% helix, 49% strand | A0A075ETL7 |
| K | B10 antibody heavy chain Fab | protein | 221 | 6% helix, 49% strand | — |
| L | B10 antibody light chain Fab | protein | 214 | 6% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, K
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.82 | 0.84 | 97 | empty |
| 2 | 361 | 0.57 | 0.75 | 43 | empty |
| 3 | 137 | 0.50 | 0.79 | 33 | empty |
| 4 | 98 | 0.37 | 0.75 | 22 | empty |
| 5 | 73 | 0.32 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- K–L · 2112 Ų buried · 19 hydrogen bonds · protein-protein
- A–K · 552 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 425 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6N6B · The complex crystal structure of neuraminidase from A/Minnesota/11/2010 with B10 antibody. · the same entry in another collection · chain A against A, 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 A0A075ETL7
- Elsewhere: RCSB PDB 6N6B · PDBe 6N6B · UniProt A0A075ETL7
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