Research workbench
Neuraminidase of A/BREVIG MISSION/1/1918 H1N1 strain in complex with zanamivir
Analyse Neuraminidase of A/BREVIG MISSION/1/1918 H1N1 strain in complex with zanamivir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B7E
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- Q9IGQ6
- Ligands
- ZMR, NAG, FUC, CA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase (EC 3.2.1.18) | protein | 385 | 3% helix, 46% strand | Q9IGQ6 |
Ligands and binding sites
- ZMR · Zanamivir · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar
- CA · Calcium ion · metal · 5 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.61 | 0.80 | 44 | ZMR |
| 2 | 185 | 0.59 | 0.82 | 31 | ZMR |
| 3 | 188 | 0.54 | 0.79 | 22 | empty |
| 4 | 98 | 0.37 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1582 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3B7E · Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir · 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 Q9IGQ6
- Elsewhere: RCSB PDB 3B7E · PDBe 3B7E · UniProt Q9IGQ6
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