1YNL: Ig gamma light chain

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. Determined by X-ray diffraction at 1.7 Å resolution. Released 16 Aug 2005.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,699
Mol. weight: 47.73 kDa
Ligands: NES
Released: 16 Aug 2005

Explore 1YNL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YNL 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.

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-40	8	8
β-strand	44-52	9	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	102	1	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
α-helix	154-156	3
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

Chain L: 8 helices, 23 β-strands

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	45-49	5	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	119-121	3
α-helix	122-126	5
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	183-186	4
β-strand	191-197	7	6
β-strand	205-210	6	6
α-helix	211-213	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ig gamma light chain	L	protein	219	Mus musculus	A2P1G9 (AlphaFold model)
Ig gamma heavy chain	H	protein	219	Mus musculus	P01867 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1YNL_1 Ig gamma light chain (chains L)
ELVMTQSPLSLPVSLGDQASISCRPSQSLVHSNGNTYLHWYLQKPGQSPKLLIYRVSNRF
SGVPDRFSGSGSGTAFTLKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLELKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1YNL_2 Ig gamma heavy chain (chains H)
RVQLLESGAELMKPGASVQISCKATGYTFSFYWIEWVKERPGHGLEWIGEILPGSGRTNY
REKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCTRGYSSMDYWGQGTSVTVSAAKTT
PPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTM
SSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPI

Ligands and cofactors

ID	Name	Formula	Copies
NES	2-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-ethanesulfonic acid	C6 H15 N O6 S	1

Primary citation

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:

1YNK 2.1 Å, Identification of Key residues of the NC6.8 Fab antibody fragment binding to synthetic…
2CGR 2.2 Å, Local and transmitted conformational changes on complexation of an anti-sweetener FAB
1CGS 2.6 Å, Local and transmitted conformational changes on complexation of an anti-sweetener FAB
4ZXB 3.3 Å, Structure of the human insulin receptor ectodomain, IRDeltabeta construct, in complex…

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