Research workbench
Crystal structure of Fab WO2 bound to the N terminal domain of amyloid beta peptide (1-28)
Analyse Crystal structure of Fab WO2 bound to the N terminal domain of amyloid beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BAE
- Type
- protein
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- WO2 IGG2A Fab fragment light chain kappa; WO2 IGG2A Fab fragment heavy chain; Amyloid…
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | WO2 IGG2A Fab fragment light chain kappa | protein | 218 | 6% helix, 52% strand | — |
| H | WO2 IGG2A Fab fragment heavy chain | protein | 219 | 7% helix, 54% strand | — |
| A | Amyloid beta peptide | protein | 7 | 0% helix, 14% strand | — |
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 | 371 | 0.54 | 0.74 | 46 | empty |
| 2 | 70 | 0.32 | 0.74 | 22 | empty |
| 3 | 76 | 0.29 | 0.72 | 20 | empty |
| 4 | 51 | 0.24 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1849 Ų buried · 19 hydrogen bonds · protein-protein
- H–A · 394 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 327 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3BAE · Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28) · 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 3BAE · PDBe 3BAE
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