Research workbench
The crystal structure of neuraminidase from A/NORTHERN PINTAIL/WASHINGTON/40964/2014 influenza virus
Analyse The crystal structure of neuraminidase from A/NORTHERN… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HUK
- Type
- protein
- Length
- 1,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- A0A0C4WXC5
- Ligands
- NAG, MAN, BMA, CA
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 388 | 3% helix, 48% strand | A0A0C4WXC5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, D, B, C
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains D, C, A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, C, A, 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
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.80 | 0.81 | 109 | empty |
| 2 | 293 | 0.69 | 0.83 | 50 | empty |
| 3 | 272 | 0.63 | 0.81 | 43 | empty |
| 4 | 271 | 0.60 | 0.79 | 40 | empty |
| 5 | 296 | 0.59 | 0.78 | 47 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1687 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1627 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1623 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1611 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5HUK · The crystal structure of neuraminidase from A/Northern pintail/Washington/40964/2014… · 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 A0A0C4WXC5
- Elsewhere: RCSB PDB 5HUK · PDBe 5HUK · UniProt A0A0C4WXC5
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