SMTL ID : 5a2l.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ASP- CYS- ARG- PRO: MODIFIED ANTIGEN TN(Non-covalent)

ALA-PRO-ASP-CYS-ARG-PRO.1: 11 residues within 4Å: Chain A: N.31, Y.32, W.33, L.53, V.101, G.102, Q.103, Y.168, W.227, W.232 Ligands: A2G.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.32, A:W.33, A:Y.168, A:W.227, A:W.227, A:W.232 Hydrogen bonds: A:N.31, A:Y.32, A:W.33, A:G.102, A:Q.103 Water bridges: A:W.33, A:R.52

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

EDO.2: 5 residues within 4Å: Chain A: S.7, G.8, K.19, L.20, S.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.7, A:K.19 EDO.3: 4 residues within 4Å: Chain A: G.68, R.69, N.86, N.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.68, A:N.87 EDO.4: 3 residues within 4Å: Chain A: G.149, E.150, T.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.151 Water bridges: A:T.151 EDO.5: 2 residues within 4Å: Chain A: S.166, N.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.166, A:N.167

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

A2G.6: 5 residues within 4Å: Chain A: W.33 Ligands: ALA-PRO-ASP-CYS-ARG-PRO.1, ALA-PRO-ASP-CYS-ARG-PRO.1, ALA-PRO-ASP-CYS-ARG-PRO.1, ALA-PRO-ASP-CYS-ARG-PRO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Saez, N. et al., Deciphering the Non-Equivalence of Serine and Threonine O-Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an Anti-Muc1 Antibody. Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2015-06-03

Peptides

SCFV-SM3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

SCFV-SM3

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