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
- 7KQG
- Type
- protein
- Length
- 663 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; 1272 Fab heavy chain; 1272 Fab light chain
- UniProt
- E1TVD5
- Ligands
- NAG, BMA, MAN
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 234 | 11% helix, 31% strand | E1TVD5 |
| B | 1272 Fab heavy chain | protein | 216 | 6% helix, 49% strand | — |
| C | 1272 Fab light chain | protein | 213 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.60 | 0.74 | 48 | empty |
| 2 | 146 | 0.43 | 0.75 | 28 | NAG |
| 3 | 86 | 0.40 | 0.78 | 26 | empty |
| 4 | 78 | 0.30 | 0.73 | 17 | empty |
| 5 | 56 | 0.30 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1832 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 765 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 104 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7KQG · 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 E1TVD5
- Elsewhere: RCSB PDB 7KQG · PDBe 7KQG · UniProt E1TVD5
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