Research workbench
Crystal structure of Fab 8F8 in complex a H2N2 influenza virus hemagglutinin
Analyse Crystal structure of Fab 8F8 in complex a H2N2 influenza virus hemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HF5
- Type
- protein
- Length
- 845 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.004
- Source
- Homo sapiens; Influenza A virus
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; Fab 8F8 heavy chain; Fab 8F8 light chain
- UniProt
- C7S226
- Ligands
- NAG, BMA, MAN
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · resolution 3.004 · 4 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 324 | 9% helix, 40% strand | C7S226 |
| B | Hemagglutinin HA2 | protein | 172 | 56% helix, 10% strand | C7S226 |
| H | Fab 8F8 heavy chain | protein | 153 | 7% helix, 42% strand | — |
| L | Fab 8F8 light chain | protein | 196 | 5% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.59 | 0.79 | 33 | empty |
| 2 | 429 | 0.58 | 0.75 | 52 | empty |
| 3 | 122 | 0.55 | 0.83 | 28 | empty |
| 4 | 181 | 0.47 | 0.76 | 33 | empty |
| 5 | 154 | 0.46 | 0.76 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2621 Ų buried · 30 hydrogen bonds · protein-protein
- H–L · 1265 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 806 Ų buried · 18 hydrogen bonds · protein-protein
- A–L · 90 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4HF5 · Crystal structure of Fab 8F8 in complex a H2N2 influenza virus 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 C7S226
- Elsewhere: RCSB PDB 4HF5 · PDBe 4HF5 · UniProt C7S226
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