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. Determined by X-ray diffraction at 2.1 Å resolution. Released 16 Aug 2005.
Explore 1YNK in 3D Show helices and sheets RCSB PDB PDBe
1YNK contains 16 α-helices and 44 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-6 | 4 | 7 |
| α-helix | 7-9 | 3 | |
| β-strand | 10-12 | 3 | 8 |
| β-strand | 18-25 | 8 | 7 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 8 |
| β-strand | 45-52 | 8 | 8 |
| β-strand | 56-59 | 4 | 8 |
| α-helix | 61-63 | 3 | |
| β-strand | 64 | 1 | 7 |
| β-strand | 67-72 | 6 | 7 |
| β-strand | 77-82 | 6 | 7 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-95 | 8 | 8 |
| β-strand | 99-102 | 4 | 8 |
| β-strand | 106-110 | 5 | 8 |
| α-helix | 113-115 | 3 | |
| β-strand | 116 | 1 | 9 |
| α-helix | 117-118 | 2 | |
| β-strand | 119-123 | 5 | 10 |
| α-helix | 129-131 | 3 | |
| β-strand | 134-144 | 11 | 10 |
| β-strand | 145 | 1 | 9 |
| β-strand | 150-153 | 4 | 11 |
| β-strand | 162-170 | 9 | 10 |
| β-strand | 173-183 | 11 | 10 |
| β-strand | 193-198 | 6 | 11 |
| α-helix | 199-201 | 3 | |
| β-strand | 203-208 | 6 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4-7 | 4 | 1 |
| β-strand | 10-13 | 4 | 2 |
| β-strand | 19-25 | 7 | 1 |
| β-strand | 27C | 1 | 3 |
| β-strand | 31 | 1 | 3 |
| β-strand | 33-38 | 6 | 2 |
| β-strand | 44-49 | 6 | 2 |
| β-strand | 53-54 | 2 | 2 |
| α-helix | 55 | 1 | |
| β-strand | 62-67 | 6 | 1 |
| β-strand | 70-75 | 6 | 1 |
| α-helix | 80-82 | 3 | |
| β-strand | 84-90 | 7 | 2 |
| α-helix | 96 | 1 | |
| β-strand | 97-98 | 2 | 2 |
| β-strand | 102-106 | 5 | 2 |
| β-strand | 111 | 1 | 4 |
| β-strand | 114-118 | 5 | 5 |
| α-helix | 122-125 | 4 | |
| β-strand | 129-139 | 11 | 5 |
| β-strand | 140 | 1 | 4 |
| β-strand | 145-150 | 6 | 6 |
| β-strand | 153-155 | 3 | 6 |
| β-strand | 159-163 | 5 | 5 |
| α-helix | 164-167 | 4 | |
| β-strand | 173-182 | 10 | 5 |
| α-helix | 183-187 | 5 | |
| β-strand | 191-197 | 7 | 6 |
| α-helix | 204 | 1 | |
| β-strand | 205-210 | 6 | 6 |
| α-helix | 211-213 | 3 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| immunoglobulin kappa light chain | L | protein | 219 | Mus musculus | A2P1G9 (AlphaFold model) |
| Ig gamma heavy chain | H | protein | 219 | Mus musculus | P01867 (AlphaFold model) |
>1YNK_1 immunoglobulin kappa light chain (chains L) ELVMTQSPLSLPVSLGDQASISCRPSQSLVHSNGNTYLHWYLQKPGQSPKLLIYRVSNRF SGVPDRFSGSGSGTAFTLKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLELKRADAAPTV SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
>1YNK_2 Ig gamma heavy chain (chains H) RVQLLESGAELMKPGASVQISCKATGYTFSEYWIEWVKERPGHGLEWIGEILPGSGRTNY REKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCTRGYSSMDYWGQGTSVTVSAAKTT PPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTM SSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPI
| ID | Name | Formula | Copies |
|---|---|---|---|
| SC5 | 2-[((R)-{[4-(AMINOMETHYL)PHENYL]AMINO}{[(1R)-1-phenylethyl]amino}methyl)amino]e… | C18 H26 N4 O2 | 1 |
Cocrystal Structures of NC6.8 Fab Identify Key Interactions for High Potency Sweetener Recognition: Implications for the Design of Synthetic Sweeteners. Gokulan, K., Khare, S., Ronning, D.R. et al. Biochemistry (2005) 44:9889-9898. DOI 10.1021/bi050613u · PubMed
Other PDB entries of the same protein (UniProt A2P1G9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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