Research workbench
Influenza hemagglutinin in complex with a neutralizing antibody
Analyse Influenza hemagglutinin in complex with a neutralizing antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UGY
- Type
- protein
- Length
- 2,781 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.801
- Source
- Homo sapiens; Influenza A virus (A/Solomon Islands/3/2006(H1N1))
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; CH65 heavy chain; CH65 light chain
- UniProt
- A7UPX0, S6C4S0, Q8N355
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.801 · 4 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 323 | 7% helix, 38% strand | A7UPX0 |
| B, D, F | Hemagglutinin HA2 | protein | 173 | 50% helix, 14% strand | A7UPX0 |
| H, I, J | CH65 heavy chain | protein | 221 | 3% helix, 50% strand | S6C4S0 |
| L, M, N | CH65 light chain | protein | 210 | 6% helix, 50% strand | Q8N355 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.87 | 0.95 | 59 | empty |
| 2 | 805 | 0.83 | 0.85 | 103 | empty |
| 3 | 179 | 0.73 | 0.90 | 31 | empty |
| 4 | 275 | 0.72 | 0.86 | 46 | empty |
| 5 | 272 | 0.72 | 0.86 | 48 | empty |
Interfaces
24 interfaces between chains.
- E–F · 2891 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2888 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2888 Ų buried · 39 hydrogen bonds · protein-protein
- J–N · 1891 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1884 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5UGY · Influenza hemagglutinin in complex with a neutralizing antibody · 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 A7UPX0
- Every structure of UniProt S6C4S0
- Every structure of UniProt Q8N355
- Elsewhere: RCSB PDB 5UGY · PDBe 5UGY · UniProt A7UPX0 · UniProt S6C4S0 · UniProt Q8N355
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