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Structure of full-length influenza HA with a head-binding antibody at pH 5.2, conformation C, central helices splay
Analyse Structure of full-length influenza HA with a head-binding antibody at pH 5.2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K3B
- Type
- protein
- Length
- 2,394 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Homo sapiens; Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
- Molecule
- Hemagglutinin; antibody Fab light chain; antibody Fab heavy chain
- UniProt
- Q91MA7, C7RWD9
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · resolution 3.4 · 4 distinct chains · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 307 | 10% helix, 39% strand | Q91MA7 |
| B, D, F | Hemagglutinin | protein | 77 | 64% helix, 3% strand | C7RWD9 |
| G, I, K | antibody Fab light chain | protein | 202 | 6% helix, 41% strand | — |
| H, J, L | antibody Fab heavy chain | protein | 212 | 8% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, C, H, B, E, J, D, L
- MAN · alpha-D-mannopyranose · sugar · 21 copies · chains H, E, A, B, J, C, D, L, F
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains C, H, E, J, A, L
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 | 896 | 0.79 | 0.82 | 65 | empty |
| 2 | 942 | 0.79 | 0.81 | 70 | empty |
| 3 | 874 | 0.78 | 0.81 | 63 | empty |
| 4 | 60 | 0.71 | 0.97 | 18 | empty |
| 5 | 66 | 0.70 | 0.97 | 21 | empty |
Interfaces
27 interfaces between chains.
- C–D · 1775 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1758 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1737 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1481 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 1472 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 7K3B · Structure of full-length influenza ha with a head-binding antibody at pH 5.2… · 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 Q91MA7
- Every structure of UniProt C7RWD9
- Elsewhere: RCSB PDB 7K3B · PDBe 7K3B · UniProt Q91MA7 · UniProt C7RWD9
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