SMTL ID : 5a2i.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

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

ALA-PRO-ASP-SER-ARG-PRO.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.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.33, A:Y.168, 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, A:G.102

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

EDO.2: 3 residues within 4Å: Chain A: N.31, L.53 Ligands: ALA-PRO-ASP-SER-ARG-PRO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.31 EDO.3: 1 residues within 4Å: Chain A: S.142 No protein-ligand interaction detected (PLIP)

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

A2G.4: 6 residues within 4Å: Chain A: W.33 Ligands: ALA-PRO-ASP-SER-ARG-PRO.1, ALA-PRO-ASP-SER-ARG-PRO.1, ALA-PRO-ASP-SER-ARG-PRO.1, ALA-PRO-ASP-SER-ARG-PRO.1, ALA-PRO-ASP-SER-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

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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