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The crystal structure of hemagglutinin from a swine influenza virus (A/SWINE/MISSOURI/2124514/2006)
Analyse The crystal structure of hemagglutinin from a swine influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W8N
- Type
- protein
- Length
- 1,471 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A9YN66
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 321 | 9% helix, 41% strand | A9YN66 |
| B | Hemagglutinin | protein | 169 | 53% helix, 13% strand | A9YN66 |
| C | Hemagglutinin | protein | 326 | 9% helix, 40% strand | A9YN66 |
| D | Hemagglutinin | protein | 172 | 52% helix, 13% strand | A9YN66 |
| E | Hemagglutinin | protein | 319 | 9% helix, 41% strand | A9YN66 |
| F | Hemagglutinin | protein | 164 | 55% helix, 12% strand | A9YN66 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.80 | 0.82 | 87 | empty |
| 2 | 122 | 0.79 | 0.97 | 22 | empty |
| 3 | 479 | 0.77 | 0.85 | 55 | empty |
| 4 | 518 | 0.76 | 0.83 | 72 | empty |
| 5 | 546 | 0.75 | 0.83 | 62 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3104 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2803 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2633 Ų buried · 32 hydrogen bonds · protein-protein
- B–F · 1262 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1259 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 4W8N · The crystal structure of hemagglutinin from a swine 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 A9YN66
- Elsewhere: RCSB PDB 4W8N · PDBe 4W8N · UniProt A9YN66
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