Research workbench
Crystal structure of the "avianized" 1918 influenza virus hemagglutinin
Analyse Crystal structure of the "avianized" 1918 influenza virus hemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GXX
- Type
- protein
- Length
- 1,482 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q9WFX3
- Ligands
- NAG, BMA, MAN
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 323 | 9% helix, 42% strand | Q9WFX3 |
| B, D | Hemagglutinin HA2 chain | protein | 170 | 56% helix, 16% strand | Q9WFX3 |
| C | Hemagglutinin HA1 chain | protein | 323 | 9% helix, 42% strand | Q9WFX3 |
| E | Hemagglutinin HA1 chain | protein | 325 | 9% helix, 41% strand | Q9WFX3 |
| F | Hemagglutinin HA2 chain | protein | 171 | 56% helix, 15% strand | Q9WFX3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, C, E, F
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.84 | 0.85 | 131 | empty |
| 2 | 198 | 0.82 | 0.96 | 26 | empty |
| 3 | 614 | 0.72 | 0.80 | 53 | empty |
| 4 | 544 | 0.71 | 0.80 | 78 | empty |
| 5 | 552 | 0.70 | 0.79 | 45 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2801 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 2740 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2723 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1199 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1192 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4GXX · Crystal structure of the "avianized" 1918 influenza virus hemagglutinin · 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 Q9WFX3
- Elsewhere: RCSB PDB 4GXX · PDBe 4GXX · UniProt Q9WFX3
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