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The crystal structure of neuraminidase from A/SICHUAN/26221/2014 influenza virus
Analyse The crystal structure of neuraminidase from A/SICHUAN/26221/2014 influenza virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HUM
- Type
- protein
- Length
- 1,556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase | protein | 389 | 3% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, B, D
- 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
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.72 | 0.99 | 20 | empty |
| 2 | 52 | 0.71 | 0.99 | 19 | empty |
| 3 | 51 | 0.70 | 0.98 | 19 | empty |
| 4 | 52 | 0.70 | 0.98 | 19 | empty |
| 5 | 325 | 0.64 | 0.80 | 51 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1716 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1699 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1692 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1674 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5HUM · The crystal structure of neuraminidase from A/Sichuan/26221/2014 influenza virus · 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
- Elsewhere: RCSB PDB 5HUM · PDBe 5HUM
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