MolNFT v1 · #19279 · protein
Influenza virus hemagglutinin complexed with a neutralizing antibody
1QFU · Protein (hemagglutinin (HA1 chain)): “Influenza virus hemagglutinin complexed with a neutralizing antibody”. X-ray diffraction, 3 ligands (NAG, NDG, BMA), 9 pockets (best druggability 0.60). MolNFT v1 #19279 on GenesisL1: 3D…
- PDB
- 1QFU
- Type
- protein
- Length
- 930 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hemagglutinin (HA1 chain)); Protein (hemagglutinin (HA2 chain)); Protein…
- UniProt
- P03437
- Ligands
- NAG, NDG, BMA
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (hemagglutinin (HA1 chain)) | protein | 317 | 9% helix, 37% strand | P03437 |
| B | Protein (hemagglutinin (HA2 chain)) | protein | 173 | 53% helix, 13% strand | P03437 |
| L | Protein (immunoglobulin IGG1-kappa antibody (light chain)) | protein | 217 | 5% helix, 39% strand | — |
| H | Protein (immunoglobulin IGG1-kappa antibody (heavy chain)) | protein | 223 | 9% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.60 | 0.79 | 47 | empty |
| 2 | 351 | 0.59 | 0.77 | 32 | empty |
| 3 | 230 | 0.47 | 0.73 | 28 | empty |
| 4 | 104 | 0.38 | 0.75 | 19 | empty |
| 5 | 79 | 0.35 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2995 Ų buried · 45 hydrogen bonds · protein-protein
- L–H · 2061 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 796 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 202 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 1QFU · Influenza virus hemagglutinin complexed 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 P03437
- Elsewhere: RCSB PDB 1QFU · PDBe 1QFU · UniProt P03437
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