Research workbench
Crystal structure of monoclonal antibody 3F8 Fab fragment that binds to GD2 ganglioside
Analyse Crystal structure of monoclonal antibody 3F8 Fab fragment that binds to GD2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VFG
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3F8 light chain; 3F8 heavy chain
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 3F8 light chain | protein | 211 | 7% helix, 53% strand | — |
| H | 3F8 heavy chain | protein | 217 | 7% helix, 50% strand | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.67 | 0.75 | 73 | empty |
| 2 | 106 | 0.39 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- L–H · 1838 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3VFG · Crystal structure of monoclonal antibody 3F8 Fab fragment that binds to GD2 ganglioside · 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 3VFG · PDBe 3VFG
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