Research workbench
Structure of the neuraminidase from the B/LYON/CHU/15.216/2011 virus in complex with oseltamivir
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
- 4CPY
- 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
- Ligands
- G39, NAG, CA
- Pockets
- 5 · best druggability 0.80
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 | — |
Ligands and binding sites
- G39 · (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy) cyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 17 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 | 138 | 0.80 | 0.97 | 28 | empty |
| 2 | 106 | 0.77 | 0.97 | 25 | empty |
| 3 | 155 | 0.55 | 0.81 | 25 | G39, EDO |
| 4 | 158 | 0.53 | 0.80 | 29 | G39 |
| 5 | 154 | 0.49 | 0.78 | 43 | EDO |
Interfaces
1 interface between chains.
- A–B · 1984 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4CPY · 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 4CPY · PDBe 4CPY
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