Research workbench
Vibrio cholerae neuraminidase complexed with zanamivir
Analyse Vibrio cholerae neuraminidase complexed with zanamivir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EKU
- Type
- protein
- Length
- 755 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase
- EC
- 3.2.1.18
- UniProt
- P0C6E9
- Ligands
- ZMR, NA, CA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase (EC 3.2.1.18) | protein | 755 | 7% helix, 52% strand | P0C6E9 |
Ligands and binding sites
- ZMR · Zanamivir · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.70 | 0.81 | 55 | GOL |
| 2 | 237 | 0.61 | 0.81 | 25 | empty |
| 3 | 124 | 0.56 | 0.84 | 25 | ZMR |
| 4 | 128 | 0.45 | 0.77 | 26 | empty |
| 5 | 115 | 0.42 | 0.76 | 23 | GOL |
Compared structures
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 P0C6E9
- Elsewhere: RCSB PDB 6EKU · PDBe 6EKU · UniProt P0C6E9
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