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The crystal structure of hemagglutinin from A/SICHUAN/26221/2014 (H5N6) influenza virus
Analyse The crystal structure of hemagglutinin from A/SICHUAN/26221/2014 (H5N6)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HU8
- Type
- protein
- Length
- 1,446 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- Ligands
- NAG, FUC
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 320 | 8% helix, 42% strand | — |
| B, D, F | Hemagglutinin HA2 | protein | 162 | 59% helix, 15% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, E
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.83 | 0.98 | 20 | empty |
| 2 | 218 | 0.82 | 0.95 | 24 | empty |
| 3 | 221 | 0.82 | 0.95 | 25 | empty |
| 4 | 227 | 0.82 | 0.94 | 29 | empty |
| 5 | 768 | 0.81 | 0.84 | 63 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2748 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2736 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2712 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 1557 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1380 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 5HU8 · The crystal structure of hemagglutinin from A/Sichuan/26221/2014 (H5N6) 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 5HU8 · PDBe 5HU8
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