SMTL ID : 6frj.1

Crystal structure of scFv-SM3 in complex with APD-SeThrGalNAc-RP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ASP- T9E- ARG- PRO- NH2: APD-SeThr-RP(Non-covalent)

ALA-PRO-ASP-T9E-ARG-PRO-NH2.1: 9 residues within 4Å: Chain A: N.31, Y.32, W.33, Q.103, Y.168, W.227, W.232 Ligands: EDO.2, A2G.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: 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:Y.32, A:W.33, A:Q.103 Water bridges: A:W.33, A:G.102, A:Y.168

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

EDO.2: 7 residues within 4Å: Chain A: G.102, Q.103, G.186, N.189 Ligands: ALA-PRO-ASP-T9E-ARG-PRO-NH2.1, ALA-PRO-ASP-T9E-ARG-PRO-NH2.1, ALA-PRO-ASP-T9E-ARG-PRO-NH2.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.103 EDO.3: 3 residues within 4Å: Chain A: T.146, S.147, E.150 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.145, A:T.146, A:T.146 EDO.4: 2 residues within 4Å: Chain A: V.152, T.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.153 EDO.5: 2 residues within 4Å: Chain A: P.195, A.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.196, A:R.197

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

A2G.6: 4 residues within 4Å: Chain A: W.33 Ligands: ALA-PRO-ASP-T9E-ARG-PRO-NH2.1, ALA-PRO-ASP-T9E-ARG-PRO-NH2.1, ALA-PRO-ASP-T9E-ARG-PRO-NH2.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.33, A:W.33, A:N.56

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

2019-02-20

Peptides

scFv-SM3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

scFv-SM3

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