Research workbench
Crystal structure of broadly neutralizing antibody F045-092 in complex with A/VICTORIA/3/1975 (H3N2) influenza hemagglutinin
Analyse Crystal structure of broadly neutralizing antibody F045-092 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O58
- Type
- protein
- Length
- 925 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Fab F045-092 light chain; Fab F045-092…
- UniProt
- P03435, P0CG05, S6C4S0
- Ligands
- NAG, MAN, BMA, SO4
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 317 | 10% helix, 41% strand | P03435 |
| B | Hemagglutinin HA2 chain | protein | 172 | 54% helix, 15% strand | P03435 |
| L | Fab F045-092 light chain | protein | 213 | 7% helix, 51% strand | P0CG05 |
| H | Fab F045-092 heavy chain | protein | 223 | 6% helix, 48% strand | S6C4S0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, L, H
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.59 | 0.80 | 37 | SO4, PEG |
| 2 | 65 | 0.55 | 0.88 | 20 | empty |
| 3 | 200 | 0.55 | 0.79 | 35 | empty |
| 4 | 180 | 0.50 | 0.77 | 25 | empty |
| 5 | 241 | 0.48 | 0.74 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2897 Ų buried · 36 hydrogen bonds · protein-protein
- L–H · 1599 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 640 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4O58 · Crystal structure of broadly neutralizing antibody F045-092 in complex with… · 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 P03435
- Every structure of UniProt P0CG05
- Every structure of UniProt S6C4S0
- Elsewhere: RCSB PDB 4O58 · PDBe 4O58 · UniProt P03435 · UniProt P0CG05 · UniProt S6C4S0
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