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
- 7KQI
- Type
- protein
- Length
- 652 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1209 Fab heavy chain; 1209 Fab light chain; Hemagglutinin
- UniProt
- A4D5Q0
- Ligands
- NAG, BMA
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1209 Fab heavy chain | protein | 216 | 6% helix, 47% strand | — |
| C | 1209 Fab light chain | protein | 211 | 5% helix, 52% strand | — |
| B | Hemagglutinin | protein | 225 | 11% helix, 31% strand | A4D5Q0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.63 | 0.75 | 59 | empty |
| 2 | 222 | 0.58 | 0.80 | 33 | empty |
| 3 | 248 | 0.50 | 0.75 | 50 | empty |
| 4 | 81 | 0.46 | 0.81 | 18 | empty |
| 5 | 99 | 0.36 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1756 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 773 Ų buried · 19 hydrogen bonds · protein-protein
- C–B · 71 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7KQI · 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 A4D5Q0
- Elsewhere: RCSB PDB 7KQI · PDBe 7KQI · UniProt A4D5Q0
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