Research workbench
Crystal structure, sequence, and epitope mapping of a peptide complex of an anti-influenza ha peptide antibody Fab 26(SLASH)9: fine-tuning antibody specificity
Analyse Crystal structure, sequence, and epitope mapping of a peptide complex of an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FRG
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A 26/9 Fab (light chain); IGG2A 26/9 Fab (heavy chain); Influenza hemagglutinin HA1…
- Ligands
- ACE, NH2
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2A 26/9 Fab (light chain) | protein | 217 | 6% helix, 52% strand | — |
| H | IGG2A 26/9 Fab (heavy chain) | protein | 220 | 7% helix, 51% strand | — |
| P | Influenza hemagglutinin HA1 (strain X47) (residues 101 - 108) | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.47 | 0.74 | 40 | empty |
| 2 | 89 | 0.46 | 0.81 | 18 | empty |
| 3 | 62 | 0.30 | 0.75 | 14 | empty |
| 4 | 64 | 0.27 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1928 Ų buried · 16 hydrogen bonds · protein-protein
- H–P · 454 Ų buried · 13 hydrogen bonds · protein-protein
- L–P · 245 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1FRG · Crystal structure, sequence, and epitope mapping of a peptide complex of an… · the same entry in another collection · chain L against L, 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 1FRG · PDBe 1FRG
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