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The crystal structure of hemagglutinin from A/GYRFALCON/WASHINGTON/41088-6/2014 influenza virus
Analyse The crystal structure of hemagglutinin from A/GYRFALCON/WASHINGTON/41088-6/2014… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HUF
- Type
- protein
- Length
- 1,500 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- A0A0C4X0C0
- Ligands
- NAG, MAN
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 324 | 6% helix, 42% strand | A0A0C4X0C0 |
| B, D, F | Hemagglutinin HA2 | protein | 176 | 51% helix, 12% strand | A0A0C4X0C0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C, B, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.86 | 0.86 | 125 | empty |
| 2 | 175 | 0.82 | 0.97 | 20 | empty |
| 3 | 275 | 0.82 | 0.93 | 32 | empty |
| 4 | 332 | 0.81 | 0.91 | 41 | empty |
| 5 | 337 | 0.80 | 0.90 | 42 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2839 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2839 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2826 Ų buried · 33 hydrogen bonds · protein-protein
- B–F · 1559 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1551 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5HUF · The crystal structure of hemagglutinin from A/gyrfalcon/Washington/41088-6/2014 influenza… · 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 A0A0C4X0C0
- Elsewhere: RCSB PDB 5HUF · PDBe 5HUF · UniProt A0A0C4X0C0
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