4D69 image
Entry Detail
PDB ID:
4D69
Keywords:
SUGAR BINDING PROTEIN
Title:
SOYBEAN AGGLUTININ FROM GLYCINE MAX IN COMPLEX WITH THE ANTIGEN Tn
Biological Source:
Source Organism:
GLYCINE MAX, SYNTHETIC CONSTRUCT
PDB Version:
Deposition Date:
2014-11-10
Release Date:
2014-11-19
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.70 Å
R-Value Free:
0.27
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 32
4D69 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:LECTIN
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L
Chain Length:253
Number of Molecules:12
Biological Source:GLYCINE MAX
UniProt ID:P05046 Pfam ID:PF00139
Polymer Type:polypeptide(L)
Description:SHORT ANTIGEN PEPTIDE
Chain IDs:M (auth: O), N (auth: P), O (auth: Q), P (auth: R), Q (auth: S), R (auth: T), S (auth: U), T (auth: V), U (auth: W), V (auth: X), W (auth: Y), X (auth: Z)
Chain Length:5
Number of Molecules:12
Biological Source:SYNTHETIC CONSTRUCT
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
THR M THR GLYCOSYLATION SITE
Ligand Molecules
A2G
MN
Primary Citation
Detection of Tumor-Associated Glycopeptides by Lectins: The Peptide Context Modulates Carbohydrate Recognition.
Acs Chem.Biol. 10 747 ? (2015)
PMID: 25457745 DOI: 10.1021/CB500855X

Abstact

Tn antigen (α-O-GalNAc-Ser/Thr) is a convenient cancer biomarker that is recognized by antibodies and lectins. This work yields remarkable results for two plant lectins in terms of epitope recognition and reveals that these receptors show higher affinity for Tn antigen when it is incorporated in the Pro-Asp-Thr-Arg (PDTR) peptide region of mucin MUC1. In contrast, a significant affinity loss is observed when Tn antigen is located in the Ala-His-Gly-Val-Thr-Ser-Ala (AHGVTSA) or Ala-Pro-Gly-Ser-Thr-Ala-Pro (APGSTAP) fragments. Our data indicate that the charged residues, Arg and Asp, present in the PDTR sequence establish noteworthy fundamental interactions with the lectin surface as well as fix the conformation of the peptide backbone, favoring the presentation of the sugar moiety toward the lectin. These results may help to better understand glycopeptide-lectin interactions and may contribute to engineer new binding sites, allowing novel glycosensors for Tn antigen detection to be designed.

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Protein

Chemical

Disease

Primary Citation of related structures
4D69