Research workbench
Crystal structure of the paraoxon-modified A.17KAPPA antibody Fab fragment
Analyse Crystal structure of the paraoxon-modified A.17KAPPA 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
- 6Y49
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A.17KAPPA antibody Fab fragment - heavy chain; A.17KAPPA antibody Fab fragment - light…
- Ligands
- DEP
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | A.17KAPPA antibody Fab fragment - heavy chain | protein | 213 | 8% helix, 51% strand | — |
| L | A.17KAPPA antibody Fab fragment - light chain | protein | 213 | 4% helix, 48% strand | — |
Ligands and binding sites
- DEP · Diethyl phosphonate · ligand · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.68 | 0.85 | 31 | DEP |
| 2 | 579 | 0.63 | 0.75 | 52 | empty |
| 3 | 52 | 0.36 | 0.79 | 16 | empty |
| 4 | 69 | 0.34 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- H–L · 1682 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6Y49 · Crystal structure of the paraoxon-modified A.17kappa antibody FAB fragment · the same entry in another collection · chain H against H, 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 6Y49 · PDBe 6Y49
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