Research workbench
Structure of the neuraminidase from the B/LYON/CHU/15.216/2011 virus in complex with zanamivir
Analyse Structure of the neuraminidase from the B/LYON/CHU/15.216/2011 virus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CPZ
- Type
- protein
- Length
- 3,120 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- Ligands
- ZMR, NAG, BMA, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Neuraminidase (EC 3.2.1.18) | protein | 390 | 2% helix, 47% strand | — |
Ligands and binding sites
- ZMR · Zanamivir · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B, C, D, E, F, G, H
- BMA · beta-D-mannopyranose · sugar · 6 copies
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.80 | 0.98 | 29 | empty |
| 2 | 137 | 0.79 | 0.97 | 28 | empty |
| 3 | 116 | 0.78 | 0.97 | 27 | empty |
| 4 | 117 | 0.78 | 0.98 | 26 | empty |
| 5 | 112 | 0.78 | 0.98 | 27 | empty |
Interfaces
13 interfaces between chains.
- A–C · 1988 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1987 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1984 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1975 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1974 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 4CPZ · Structure of the Neuraminidase from the B/Lyon/CHU/15.216/2011 virus in complex with… · 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
- Elsewhere: RCSB PDB 4CPZ · PDBe 4CPZ
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