Research workbench
Crystal structure of the paraoxon-modified A.17 antibody Fab fragment - L47K mutant
Analyse Crystal structure of the paraoxon-modified A.17 antibody Fab fragment - L47K… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y1M
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab A.17 L47K mutant heavy chain; Fab A.17 L47K mutant light chain
- Ligands
- DEP
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab A.17 L47K mutant heavy chain | protein | 218 | 10% helix, 51% strand | — |
| L | Fab A.17 L47K mutant light chain | protein | 215 | 8% helix, 50% 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.64 | 0.74 | 65 | empty |
| 2 | 197 | 0.62 | 0.82 | 29 | DEP |
| 3 | 59 | 0.43 | 0.83 | 24 | empty |
Interfaces
1 interface between chains.
- H–L · 1897 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6Y1M · Crystal structure of the paraoxon-modified A.17 antibody FAB fragment - L47K mutant · 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 6Y1M · PDBe 6Y1M
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.