Research workbench
Crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin
Analyse Crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GXU
- Type
- protein
- Length
- 4,804 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Antibody 1F1, heavy chain; Antibody…
- UniProt
- Q9WFX3
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin HA1 chain | protein | 325 | 9% helix, 41% strand | Q9WFX3 |
| B, D, F, H, J, L | Hemagglutinin HA2 chain | protein | 171 | 57% helix, 15% strand | Q9WFX3 |
| M, Q | Antibody 1F1, heavy chain | protein | 228 | 5% helix, 50% strand | — |
| N, R | Antibody 1F1, light chain | protein | 214 | 7% helix, 51% strand | — |
| O, S, U, W | Antibody 1F1, heavy chain | protein | 125 | 5% helix, 49% strand | — |
| P, T, V, X | Antibody 1F1, light chain | protein | 111 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, C, E, G, I, K, B, D, F, H, J, L
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains M, O, Q, S, U, W
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 | 1044 | 0.88 | 0.90 | 143 | empty |
| 2 | 499 | 0.87 | 0.93 | 78 | empty |
| 3 | 433 | 0.77 | 0.86 | 58 | empty |
| 4 | 1085 | 0.74 | 0.77 | 112 | empty |
| 5 | 567 | 0.72 | 0.80 | 51 | empty |
Interfaces
58 interfaces between chains.
- C–D · 2858 Ų buried · 44 hydrogen bonds · protein-protein
- I–J · 2830 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2810 Ų buried · 50 hydrogen bonds · protein-protein
- K–L · 2792 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 2773 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 disulfide, 18 glycan, 12 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4GXU · Crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin · 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 Q9WFX3
- Elsewhere: RCSB PDB 4GXU · PDBe 4GXU · UniProt Q9WFX3
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