SMTL ID : 5fxc.1

Crystal structure of glycopeptide 22 in complex with scFv-SM3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ASP- THR- ARG- PRO: GLYCOPEPTIDE(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: EDO.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.32, A:W.33, A:Y.168, A:Y.168, A:W.227, A:W.227, A:W.232 Hydrogen bonds: A:N.31, A:Y.32, A:W.33, A:Q.103, A:Y.168 Water bridges: A:W.33, A:G.102

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

EDO.2: 5 residues within 4Å: Chain A: V.137, V.138, V.233, F.234, G.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.136, A:V.138 Water bridges: A:V.138, A:G.236 EDO.3: 6 residues within 4Å: Chain A: L.45, E.46, W.47, W.232, V.233, F.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.47, A:W.47, A:F.234 EDO.4: 5 residues within 4Å: Chain A: G.102, Q.103, G.186 Ligands: ALA-PRO-ASP-THR-ARG-PRO.1, ALA-PRO-ASP-THR-ARG-PRO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.103 EDO.5: 4 residues within 4Å: Chain A: S.25, G.26, F.27, S.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.26, A:F.27, A:S.79, A:S.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rojas-Ocariz, V. et al., Design of Alpha-S-Glycopeptides Derived from Muc1 with a Flexible and Solvent Exposed Sugar Moiety. J.Org.Chem. (2016)

Release Date

2016-06-29

Peptides

SCFV-SM3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

SCFV-SM3

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