Research workbench
Structure of neuraminidase from english duck subtype N6 complexed with 30 mm zanamivir, crystal soaked for 3 hours at 291 K.
Analyse Structure of neuraminidase from english duck subtype N6 complexed with 30 mm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CML
- Type
- protein
- Length
- 1,556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- Q6XV27
- Ligands
- ZMR, NAG, MAN, BMA, CA
- Pockets
- 17 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 389 | 3% helix, 41% strand | Q6XV27 |
Ligands and binding sites
- ZMR · Zanamivir · ligand · 8 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, C, D, B
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains A, C, B, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, A, D, B
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.66 | 0.94 | 25 | empty |
| 2 | 276 | 0.64 | 0.81 | 42 | ZMR |
| 3 | 232 | 0.63 | 0.82 | 41 | empty |
| 4 | 210 | 0.62 | 0.82 | 42 | empty |
| 5 | 271 | 0.62 | 0.81 | 36 | ZMR |
Interfaces
6 interfaces between chains.
- C–D · 1771 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1768 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1753 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1739 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 2CML · Structure of Neuraminidase from English Duck Subtype N6 Complexed with 30 MM 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 Q6XV27
- Elsewhere: RCSB PDB 2CML · PDBe 2CML · UniProt Q6XV27
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