Research workbench
Structure of neuraminidase from english duck subtype N6 complexed with 30 mm sialic acid (nana, NEU5AC), crystal soaked for 43 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
- 1W21
- 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
- 16 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 389 | 3% helix, 44% 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 · 11 copies · chains C, A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, A, B, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.66 | 0.79 | 61 | empty |
| 2 | 288 | 0.64 | 0.81 | 47 | SIA |
| 3 | 255 | 0.63 | 0.81 | 41 | SIA |
| 4 | 255 | 0.62 | 0.81 | 37 | SIA |
| 5 | 290 | 0.62 | 0.80 | 33 | SIA |
Interfaces
6 interfaces between chains.
- C–D · 1760 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1752 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1748 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1745 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 1W21 · 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 1W21 · PDBe 1W21 · UniProt Q6XV27
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