MolNFT v1 · #25658 · protein
Structure of neuraminidase from english duck subtype N6 complexed with 30 mm sialic acid (nana, NEU5AC), crystal soaked for 3 hours at 277 K.
1W1X: “Structure of neuraminidase from english duck subtype N6 complexed with 30 mm sialic acid (nana, NEU5AC)…”. X-ray diffraction, 5 ligands (NAG, MAN, SIA), 17 pockets (best druggability 0.71). MolNFT v1 #25658 on GenesisL1: 3D…
- PDB
- 1W1X
- 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
- NAG, MAN, SIA, BMA, CA
- Pockets
- 17 · best druggability 0.71
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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, D, C
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A, B, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.71 | 0.98 | 19 | empty |
| 2 | 50 | 0.67 | 0.96 | 18 | empty |
| 3 | 250 | 0.65 | 0.83 | 41 | PEG |
| 4 | 305 | 0.65 | 0.81 | 41 | SIA |
| 5 | 292 | 0.64 | 0.81 | 49 | SIA |
Interfaces
6 interfaces between chains.
- C–D · 1768 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1755 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1742 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1742 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1W1X · Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid… · 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 1W1X · PDBe 1W1X · UniProt Q6XV27
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