Research workbench
Fab fragment of 3D6 in complex with amyloid beta 1-7
Analyse Fab fragment of 3D6 in complex with amyloid beta 1-7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ONF
- Type
- protein
- Length
- 436 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3D6 Fab antibody heavy chain; 3D6 Fab antibody light chain; Amyloid beta A4 protein
- UniProt
- P05067
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 3D6 Fab antibody heavy chain | protein | 212 | 7% helix, 54% strand | — |
| L | 3D6 Fab antibody light chain | protein | 218 | 6% helix, 52% strand | — |
| P | Amyloid beta A4 protein | protein | 6 | 50% helix, 0% strand | P05067 |
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 | 138 | 0.47 | 0.78 | 27 | empty |
| 2 | 236 | 0.47 | 0.73 | 33 | empty |
| 3 | 55 | 0.32 | 0.77 | 14 | empty |
| 4 | 50 | 0.25 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1732 Ų buried · 17 hydrogen bonds · protein-protein
- H–P · 343 Ų buried · 6 hydrogen bonds · protein-protein
- L–P · 291 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P05067
- Elsewhere: RCSB PDB 4ONF · PDBe 4ONF · UniProt P05067
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