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The crystal structure of hemagglutinin from A/JIANGXI-DONGHU/346/2013 influenza virus
Analyse The crystal structure of hemagglutinin from A/JIANGXI-DONGHU/346/2013 influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WSX
- Type
- protein
- Length
- 5,892 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W | Hemagglutinin HA1 chain | protein | 319 | 9% helix, 40% strand | — |
| B, D, F, H, J, L, N, P, R, T, V, X | Hemagglutinin HA2 chain | protein | 172 | 55% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, O, B, W, X, C, U, D, M, N, E, S, F, K, L, G, Q, H, I, J, P, R, T, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.85 | 0.93 | 41 | empty |
| 2 | 450 | 0.85 | 0.92 | 45 | empty |
| 3 | 449 | 0.85 | 0.92 | 42 | empty |
| 4 | 451 | 0.84 | 0.91 | 42 | empty |
| 5 | 174 | 0.84 | 0.98 | 24 | empty |
Interfaces
70 interfaces between chains.
- S–T · 3213 Ų buried · 44 hydrogen bonds · protein-protein
- Q–R · 3212 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 3212 Ų buried · 44 hydrogen bonds · protein-protein
- O–P · 3211 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3208 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 4WSX · The crystal structure of hemagglutinin from A/Jiangxi-Donghu/346/2013 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 4WSX · PDBe 4WSX
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