Research workbench
Antibody Fab fragment
Analyse Antibody Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VG0
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal antibody 9F8 Fab fragment L chain; Monoclonal antibody 9F8 Fab fragment H chain
- Ligands
- NAG, FUC, SO4
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Monoclonal antibody 9F8 Fab fragment L chain | protein | 213 | 6% helix, 51% strand | — |
| H | Monoclonal antibody 9F8 Fab fragment H chain | protein | 219 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L
- SO4 · Sulfate ion · ion · chains H
- ACT · Acetate ion · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.54 | 0.74 | 41 | empty |
| 2 | 212 | 0.50 | 0.76 | 30 | empty |
| 3 | 62 | 0.48 | 0.85 | 23 | ACT |
| 4 | 205 | 0.43 | 0.73 | 32 | empty |
| 5 | 51 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- L–H · 1794 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3VG0 · Antibody Fab fragment · 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 3VG0 · PDBe 3VG0
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