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Identification of key residues of the NC6.8 Fab antibody fragment binding to synthetic sweeterners: crystal structure of NC6.8 co- crystalized with high potency sweetener compound SC45647
Analyse Identification of key residues of the NC6.8 Fab antibody fragment binding to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YNL
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma light chain; Ig gamma heavy chain
- UniProt
- Q6PJB2
- Ligands
- NES
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Ig gamma light chain | protein | 219 | 7% helix, 51% strand | — |
| H | Ig gamma heavy chain | protein | 219 | 7% helix, 53% strand | Q6PJB2 |
Ligands and binding sites
- NES · 2-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-ethanesulfonic acid · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.61 | 0.74 | 51 | empty |
| 2 | 70 | 0.49 | 0.84 | 19 | NES |
| 3 | 134 | 0.46 | 0.77 | 21 | empty |
| 4 | 110 | 0.39 | 0.75 | 25 | empty |
| 5 | 79 | 0.38 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- L–H · 1830 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1YNL · Identification of Key residues of the NC6.8 Fab antibody fragment binding to synthetic… · 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
- Every structure of UniProt Q6PJB2
- Elsewhere: RCSB PDB 1YNL · PDBe 1YNL · UniProt Q6PJB2
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