Research workbench
Influenza B virus neuraminidase can synthesize its own inhibitor
Analyse Influenza B virus neuraminidase can synthesize its own inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NSD
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- P27907
- Ligands
- DAN, NAG, CA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase (EC 3.2.1.18) | protein | 390 | 2% helix, 48% strand | P27907 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.79 | 0.98 | 29 | empty |
| 2 | 126 | 0.79 | 0.97 | 29 | empty |
| 3 | 189 | 0.58 | 0.81 | 27 | DAN |
| 4 | 170 | 0.56 | 0.81 | 29 | DAN |
| 5 | 200 | 0.51 | 0.77 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 1997 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1NSD · Influenza B virus neuraminidase can synthesize its own inhibitor · the same entry in another collection · chain B against B, 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 P27907
- Elsewhere: RCSB PDB 1NSD · PDBe 1NSD · UniProt P27907
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