Research workbench
The structure of hemagglutininfrom a swine-origin H4N6 influenza virus
Analyse The structure of hemagglutininfrom a swine-origin H4N6 influenza virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XL2
- Type
- protein
- Length
- 1,456 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q9E148
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin | protein | 486 | 24% helix, 29% strand | Q9E148 |
| C | Hemagglutinin | protein | 484 | 24% helix, 29% strand | Q9E148 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.84 | 0.91 | 35 | empty |
| 2 | 755 | 0.79 | 0.83 | 69 | empty |
| 3 | 715 | 0.78 | 0.83 | 79 | empty |
| 4 | 662 | 0.78 | 0.83 | 77 | empty |
| 5 | 834 | 0.75 | 0.79 | 79 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2275 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2274 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2160 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5XL2 · The structure of hemagglutininfrom a swine-origin H4N6 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
- Every structure of UniProt Q9E148
- Elsewhere: RCSB PDB 5XL2 · PDBe 5XL2 · UniProt Q9E148
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