SMTL ID : 5n7b.1

Understanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ASP- CG6- ARG- PRO- NH2: APD(CG6)RP(NH2) peptide(Non-covalent)

ALA-PRO-ASP-CG6-ARG-PRO-NH2.1: 9 residues within 4Å: Chain A: N.31, Y.32, W.33, L.53, Q.103, Y.168, W.227, W.232 Ligands: A2G.9 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.32, A:W.33, A:Y.168, A:Y.168, A:Y.168, A:W.227, A:W.232 Hydrogen bonds: A:N.31, A:Y.32, A:W.33, A:Q.103 Water bridges: A:N.31, A:R.52, A:G.102, A:Y.168, A:Y.168

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 1 residues within 4Å: Chain A: Q.215 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.215, A:E.217 EDO.3: 6 residues within 4Å: Chain A: Q.173, K.175, T.181, L.183, P.195, F.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.173, A:T.181, A:R.197 Water bridges: A:K.175 EDO.4: 5 residues within 4Å: Chain A: S.30, N.31, L.53, K.54, S.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.31, A:S.55 EDO.5: 4 residues within 4Å: Chain A: I.51, Y.58, S.73, R.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.74 Water bridges: A:I.72 EDO.6: 7 residues within 4Å: Chain A: L.45, E.46, W.47, W.232, V.233, F.234 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.45, A:W.47, A:W.232, A:F.234 EDO.7: 3 residues within 4Å: Chain A: G.186, N.188, N.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.186, A:N.189 Water bridges: A:T.187, A:N.188 EDO.8: 7 residues within 4Å: Chain A: K.43, G.44, L.45, F.234, G.235, G.236 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.45, A:L.45

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-functional Binders)

A2G.9: 3 residues within 4Å: Ligands: ALA-PRO-ASP-CG6-ARG-PRO-NH2.1, ALA-PRO-ASP-CG6-ARG-PRO-NH2.1, ALA-PRO-ASP-CG6-ARG-PRO-NH2.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Companon, I. et al., Structure-Based Design of Potent Tumor-Associated Antigens: Modulation of Peptide Presentation by Single-Atom O/S or O/Se Substitutions at the Glycosidic Linkage. J.Am.Chem.Soc. (2019)

Release Date

2018-06-27

Peptides

Ig heavy chain V-III region J606,Ig lambda-1 chain V region S43: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

Ig heavy chain V-III region J606,Ig lambda-1 chain V region S43

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