MolNFT v1 · #88270 · protein
Structure of the neuraminidase from the B/BRISBANE/60/2008 virus in complex with zanamivir
4CPN: “Structure of the neuraminidase from the B/BRISBANE/60/2008 virus in complex with zanamivir”. X-ray diffraction, 5 ligands (ZMR, NAG, BMA), 5 pockets (best druggability 0.78). MolNFT v1 #88270 on GenesisL1: 3D structure, binding…
- PDB
- 4CPN
- 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
- C0LT34
- Ligands
- ZMR, NAG, BMA, MAN, CA
- Pockets
- 5 · best druggability 0.78
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 | C0LT34 |
Ligands and binding sites
- ZMR · Zanamivir · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.78 | 0.96 | 28 | empty |
| 2 | 97 | 0.77 | 0.98 | 27 | empty |
| 3 | 193 | 0.60 | 0.82 | 29 | ZMR |
| 4 | 201 | 0.59 | 0.81 | 31 | ZMR |
| 5 | 152 | 0.49 | 0.78 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1983 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4CPN · Structure of the Neuraminidase from the B/Brisbane/60/2008 virus 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 C0LT34
- Elsewhere: RCSB PDB 4CPN · PDBe 4CPN · UniProt C0LT34
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