SMTL ID : 5a2k.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ASP- THR- ARG- PRO: ANTIGEN TN, THR IS COVALENTLY BOUND TO GALNAC(Non-covalent)

ALA-PRO-ASP-THR-ARG-PRO.1: 10 residues within 4Å: Chain A: N.31, Y.32, W.33, Q.103, Y.168, W.227, W.232 Ligands: EDO.3, EDO.5, A2G.8 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.32, A:W.33, A:Y.168, A:Y.168, A:W.227, A:W.232 Hydrogen bonds: A:Y.32, A:W.33, A:Q.103, A:Y.168 Water bridges: A:N.31, A:Y.32, A:W.33, A:R.52, A:G.102 pi-Cation interactions: A:Y.32

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

EDO.2: 2 residues within 4Å: Chain A: G.186, N.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.188 EDO.3: 3 residues within 4Å: Chain A: S.166, Y.168 Ligands: ALA-PRO-ASP-THR-ARG-PRO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.166 EDO.4: 3 residues within 4Å: Chain A: L.144, V.152, T.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.153 EDO.5: 6 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, ALA-PRO-ASP-THR-ARG-PRO.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.103, A:Q.103 Water bridges: A:G.102 EDO.6: 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:S.30, A:S.55, A:S.55 Water bridges: A:K.54 EDO.7: 5 residues within 4Å: Chain A: I.95, Q.109, G.110, D.177, H.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.110, A:D.177

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

A2G.8: 6 residues within 4Å: Chain A: W.33, Y.168 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.168

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

IG LAMBDA-1 CHAIN V REGION S43: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

IG LAMBDA-1 CHAIN V REGION S43

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