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Structure of full-length influenza ha with a head-binding antibody at pH 5.2, conformation a, neutral pH-like
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
- 7K39
- Type
- protein
- Length
- 2,712 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody Fab light chain; Antibody Fab heavy chain
- UniProt
- Q91MA7, C7RWD9
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 318 | 9% helix, 41% strand | Q91MA7 |
| B, D, F | Hemagglutinin | protein | 172 | 51% helix, 12% strand | C7RWD9 |
| G, I, K | Antibody Fab light chain | protein | 202 | 6% helix, 42% strand | — |
| H, J, L | Antibody Fab heavy chain | protein | 212 | 8% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, C, H, B, E, J, D, L, F
- 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 | 1042 | 0.86 | 0.87 | 118 | empty |
| 2 | 212 | 0.84 | 0.97 | 32 | empty |
| 3 | 901 | 0.79 | 0.82 | 71 | empty |
| 4 | 866 | 0.79 | 0.82 | 63 | empty |
| 5 | 1135 | 0.78 | 0.80 | 82 | empty |
Interfaces
27 interfaces between chains.
- E–F · 2924 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2917 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2900 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 1558 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 1547 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 7K39 · 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 7K39 · PDBe 7K39 · UniProt Q91MA7 · UniProt C7RWD9
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