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The crystal structure of hemagglutinin from A/TAIWAN/1/2013 in complex with 3'SLN
Analyse The crystal structure of hemagglutinin from A/TAIWAN/1/2013 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WSU
- Type
- protein
- Length
- 1,485 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- Ligands
- NAG, SIA, GAL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 325 | 10% helix, 39% strand | — |
| B, D, F | Hemagglutinin HA2 chain | protein | 170 | 55% helix, 14% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
- GAL · beta-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.80 | 0.87 | 83 | empty |
| 2 | 122 | 0.80 | 0.98 | 17 | empty |
| 3 | 144 | 0.78 | 0.95 | 23 | empty |
| 4 | 179 | 0.71 | 0.88 | 32 | empty |
| 5 | 165 | 0.70 | 0.89 | 31 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2805 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2797 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2786 Ų buried · 44 hydrogen bonds · protein-protein
- D–F · 1297 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1266 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4WSU · The crystal structure of hemagglutinin from A/Taiwan/1/2013 in complex with 3'SLN · 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 4WSU · PDBe 4WSU
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