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Influenza virus hemagglutinin complexed with an antibody that prevents the hemagglutinin low pH fusogenic transition
Analyse Influenza virus hemagglutinin complexed with an antibody that prevents the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KEN
- Type
- protein
- Length
- 2,351 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; Influenza virus infectivity neutralizing antibody…
- UniProt
- P03437
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 320 | 9% helix, 35% strand | — |
| B, D, F | Hemagglutinin HA2 | protein | 175 | 42% helix, 6% strand | P03437 |
| L, U | Influenza virus infectivity neutralizing antibody (light chain) | protein | 213 | 4% helix, 34% strand | — |
| H | Influenza virus infectivity neutralizing antibody (heavy chain) | protein | 221 | 1% helix, 34% strand | — |
| T | Influenza virus infectivity neutralizing antibody (heavy chain) | protein | 219 | 3% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, E, C, H, T
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains E, A, T
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 | 422 | 0.88 | 0.96 | 43 | empty |
| 2 | 269 | 0.83 | 0.95 | 25 | empty |
| 3 | 1044 | 0.81 | 0.82 | 123 | empty |
| 4 | 1098 | 0.74 | 0.77 | 104 | empty |
| 5 | 189 | 0.72 | 0.89 | 28 | empty |
Interfaces
24 interfaces between chains.
- E–F · 2965 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2955 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2949 Ų buried · 31 hydrogen bonds · protein-protein
- L–H · 2109 Ų buried · 12 hydrogen bonds · protein-protein
- U–T · 2004 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1KEN · Influenza virus hemagglutinin complexed with an antibody that prevents the hemagglutinin… · the same entry in another collection · chain C against C, 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 P03437
- Elsewhere: RCSB PDB 1KEN · PDBe 1KEN · UniProt P03437
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