Research workbench
Crystal structure of multidonor HV6-1-class broadly neutralizing influenza a antibody 56.A.09 isolated following H5 immunization.
Analyse Crystal structure of multidonor HV6-1-class broadly neutralizing influenza a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K9J
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 56.A.09 heavy chain; 56.A.09 light chain
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 56.A.09 heavy chain | protein | 228 | 7% helix, 56% strand | — |
| L | 56.A.09 light chain | protein | 212 | 7% helix, 55% strand | — |
Ligands and binding sites
- 15P · Polyethylene glycol (N=34) · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.52 | 0.73 | 47 | 15P |
| 2 | 90 | 0.41 | 0.77 | 19 | empty |
| 3 | 96 | 0.34 | 0.74 | 17 | empty |
| 4 | 65 | 0.31 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- H–L · 1990 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5K9J · Crystal structure of multidonor HV6-1-class broadly neutralizing Influenza A antibody… · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 5K9J · PDBe 5K9J
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