MolNFT v1 · #12364 · protein
Influenza virus hemagglutinin complexed with an antibody that prevents the hemagglutinin low pH fusogenic transition
1KEN · Hemagglutinin HA1: “Influenza virus hemagglutinin complexed with an antibody that prevents the hemagglutinin low pH fusogenic…”. X-ray diffraction, 2 ligands (NAG, MAN), 20 pockets (best druggability 0.88). MolNFT v1 #12364 on…
- 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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