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Crystal structure of the A/HONG KONG/1/1968 (H3N2) influenza virus hemagglutinin in complex with the antiviral drug arbidol
Analyse Crystal structure of the A/HONG KONG/1/1968 (H3N2) influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T6N
- Type
- protein
- Length
- 1,467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- Q91MA7, P03436
- Ligands
- 75U, NAG, BMA, MAN, SO4
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hemagglutinin HA1 | protein | 318 | 9% helix, 42% strand | Q91MA7 |
| B | Hemagglutinin HA2 | protein | 172 | 52% helix, 15% strand | P03436 |
| C | Hemagglutinin HA1 | protein | 317 | 9% helix, 41% strand | Q91MA7 |
| D, F | Hemagglutinin HA2 | protein | 171 | 54% helix, 13% strand | P03436 |
Ligands and binding sites
- 75U · ethyl 6-bromo-4-[(dimethylamino)methyl]-5-hydroxy-1-methyl-2-[(phenylsulfanyl)methyl]-1H-indole-3-carboxylate · ligand · 3 copies · chains A, B, E, F, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, C, B, D, E, F
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, E, A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- SO4 · Sulfate ion · ion · 4 copies · chains B, F, D, A, C
- GOL · Glycerol · additive · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.86 | 0.88 | 41 | empty |
| 2 | 265 | 0.84 | 0.95 | 30 | empty |
| 3 | 927 | 0.76 | 0.79 | 102 | SO4 |
| 4 | 496 | 0.74 | 0.82 | 55 | 75U |
| 5 | 88 | 0.74 | 0.96 | 23 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2957 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2887 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2854 Ų buried · 35 hydrogen bonds · protein-protein
- B–F · 1476 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1459 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 5T6N · Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in… · 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 Q91MA7
- Every structure of UniProt P03436
- Elsewhere: RCSB PDB 5T6N · PDBe 5T6N · UniProt Q91MA7 · UniProt P03436
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