Research workbench
Antibodies that engage the hemagglutinin receptor-binding site of influenza B viruses
Analyse Antibodies that engage the hemagglutinin receptor-binding site of influenza B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KQH
- Type
- protein
- Length
- 1,335 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; 2365 Fab heavy chain; 2365 Fab light chain
- UniProt
- A0A4P8YRB6
- Ligands
- NAG, BMA, MAN
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin | protein | 237 | 10% helix, 30% strand | A0A4P8YRB6 |
| H | 2365 Fab heavy chain | protein | 225 | 4% helix, 45% strand | — |
| L | 2365 Fab light chain | protein | 215 | 5% helix, 42% strand | — |
| C | 2365 Fab heavy chain | protein | 214 | 3% helix, 47% strand | — |
| D | 2365 Fab light chain | protein | 207 | 5% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.73 | 0.96 | 19 | empty |
| 2 | 830 | 0.71 | 0.77 | 60 | empty |
| 3 | 537 | 0.62 | 0.75 | 57 | empty |
| 4 | 131 | 0.58 | 0.84 | 18 | empty |
| 5 | 54 | 0.52 | 0.88 | 22 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1861 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1841 Ų buried · 20 hydrogen bonds · protein-protein
- H–B · 848 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 823 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 744 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7KQH · Antibodies that engage the hemagglutinin receptor-binding site of influenza B viruses · 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 A0A4P8YRB6
- Elsewhere: RCSB PDB 7KQH · PDBe 7KQH · UniProt A0A4P8YRB6
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