MolNFT v1 · #59001 · protein
Crystal structure of Fab WO2 bound to the N terminal domain of amyloid beta peptide (1-16)
3BKJ · WO2 IGG2A Fab fragment light chain kappa: “Crystal structure of Fab WO2 bound to the N terminal domain of amyloid beta peptide (1-16)”. X-ray diffraction, 3 pockets (best druggability 0.53). MolNFT v1 #59001 on GenesisL1: 3D…
- PDB
- 3BKJ
- Type
- protein
- Length
- 449 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
- 3 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | WO2 IGG2A Fab fragment light chain kappa | protein | 218 | 7% helix, 51% strand | — |
| H | WO2 IGG2A Fab fragment heavy chain | protein | 224 | 10% helix, 51% strand | — |
| A | Amyloid beta peptide | protein | 7 | 0% helix, 14% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.53 | 0.74 | 50 | empty |
| 2 | 61 | 0.30 | 0.74 | 19 | empty |
| 3 | 59 | 0.26 | 0.72 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1946 Ų buried · 19 hydrogen bonds · protein-protein
- H–A · 394 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 329 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3BKJ · Crystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16) · 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 3BKJ · PDBe 3BKJ
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