SMTL ID : 6tgg.1

scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ASP- THR- ARG- PRO: Mucin-1(Non-covalent)

ALA-PRO-ASP-THR-ARG-PRO.1: 8 residues within 4Å: Chain A: N.31, Y.32, W.33, Q.103, Y.168, W.227, W.232 Ligands: N8W.6 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:W.33, A:Q.103, A:Y.168 Water bridges: A:R.52, A:G.102, A:G.102

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

EDO.2: 5 residues within 4Å: Chain A: S.30, N.31, L.53, K.54, S.55 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.31, A:S.55, A:S.55 Water bridges: A:K.54 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 Water bridges: A:Q.173, A:K.175, A:R.197 EDO.4: 3 residues within 4Å: Chain A: T.146, S.147, E.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.146, A:S.147 Water bridges: A:E.150 EDO.5: 1 residues within 4Å: Chain A: Q.215 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.215, A:E.217

1 x N8W: ~{N}-[(6~{S},7~{R},8~{S},8~{a}~{R})-7,8-bis(oxidanyl)-3-oxidanylidene-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyridin-6-yl]ethanamide(Non-covalent)

N8W.6: 6 residues within 4Å: Chain A: W.33 Ligands: ALA-PRO-ASP-THR-ARG-PRO.1, ALA-PRO-ASP-THR-ARG-PRO.1, ALA-PRO-ASP-THR-ARG-PRO.1, ALA-PRO-ASP-THR-ARG-PRO.1, ALA-PRO-ASP-THR-ARG-PRO.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bermejo, I.A. et al., Synthesis, conformational analysis and in vivo assays of an anti-cancer vaccine that features an unnatural antigen based on an sp 2 -iminosugar fragment. Chem Sci (2020)

Release Date

2020-04-08

Peptides

ScFv_SM3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

ScFv_SM3

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