8I7P image
Deposition Date 2023-02-01
Release Date 2023-09-20
Last Version Date 2024-10-09
Entry Detail
PDB ID:
8I7P
Keywords:
Title:
Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-tyrosine
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.60 Å
R-Value Free:
0.23
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 41 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ricin A chain
Chain IDs:A
Chain Length:274
Number of Molecules:1
Biological Source:Ricinus communis
Polymer Type:polypeptide(L)
Molecule:6-(2-ethyl-4-hydroxyphenyl)-1H-indazole-3-carboxamide
Chain IDs:B
Chain Length:3
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
Crystal structure of ricin toxin A chain complexed with a highly potent pterin-based small-molecular inhibitor.
J Enzyme Inhib Med Chem 38 2219038 2219038 (2023)
PMID: 37259593 DOI: 10.1080/14756366.2023.2219038

Abstact

Ricin toxin A chain (RTA), from Ricinus communis, is a deadly protein that inactivates ribosomes by degrading an adenine residue at position 4324 in 28S rRNA. Recently, we have demonstrated that pterin-7-carboxamides with peptide pendants were potent RTA inhibitors. Among these, N-(pterin-7-carbonyl)glycyl-L-tyrosine (7PCGY) is the most potent RTA inhibitor as a small organic molecule. However, despite this fascinating inhibitory activity, the mode of interaction of 7PCGY with RTA remains elusive. This study aimed to elucidate the factors responsible for the high RTA inhibitory activity of 7PCGY based on X-ray crystallographic analysis. Herein, we report the successfully resolved X-ray crystal structure of 7PCGY/RTA complexes, revealing that the interaction between the phenolic hydroxy group in 7PCGY and Asn78 of RTA through a hydrogen bonding and the conformational change of Tyr80 and Asn122 are responsible for the high RTA inhibitory activity of 7PCGY.

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Primary Citation of related structures