MolNFT v1 · #28745 · protein
Identification of key residues of the NC6.8 Fab antibody fragment binding to synthetic sweeteners: crystal structure of NC6.8 co- crystalized with high potency sweetener compound SC45647
1YNK · Immunoglobulin kappa light chain: “Identification of key residues of the NC6.8 Fab antibody fragment binding to synthetic sweeteners: crystal…”. X-ray diffraction, 1 ligand (SC5), 5 pockets (best druggability 0.57). MolNFT v1 #28745…
- PDB
- 1YNK
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin kappa light chain; Ig gamma heavy chain
- UniProt
- Q6PJB2
- Ligands
- SC5
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin kappa light chain | protein | 219 | 7% helix, 51% strand | — |
| H | Ig gamma heavy chain | protein | 219 | 5% helix, 54% strand | Q6PJB2 |
Ligands and binding sites
- SC5 · 2-[((R)-{[4-(aminomethyl)phenyl]amino}{[(1r)-1-phenylethyl]amino}methyl)amino]ethane-1,1-diol · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.57 | 0.73 | 50 | empty |
| 2 | 118 | 0.45 | 0.78 | 21 | empty |
| 3 | 114 | 0.40 | 0.76 | 27 | empty |
| 4 | 67 | 0.40 | 0.80 | 21 | SC5 |
| 5 | 58 | 0.26 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- L–H · 1806 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1YNK · 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 1YNK · PDBe 1YNK · UniProt Q6PJB2
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