7Y4K | pdb_00007y4k

Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-ornitine

• PDB DOI: https://doi.org/10.2210/pdb7Y4K/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Ricinus communis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-15 Released: 2022-11-16 
• Deposition Author(s): Katakura, S., Goto, M., Ohba, T., Kawata, R., Nagatsu, K., Higashi, S., Matsumoto, K., Kurisu, K., Ohtsuka, K., Saito, R.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Pterin-based small molecule inhibitor capable of binding to the secondary pocket in the active site of ricin-toxin A chain.

Saito, R., Goto, M., Katakura, S., Ohba, T., Kawata, R., Nagatsu, K., Higashi, S., Kurisu, K., Matsumoto, K., Ohtsuka, K.

(2022) PLoS One 17: e0277770-e0277770

• PubMed: 36508422 
• DOI: https://doi.org/10.1371/journal.pone.0277770
• Primary Citation Related Structures: 
  7Y4K, 7Y4M


• PubMed Abstract: 
  

  The Ricin toxin A chain (RTA), which depurinates an adenine base at a specific region of the ribosome leading to death, has two adjacent specificity pockets in its active site. Based on this structural information, many attempts have been made to develop small-molecule RTA inhibitors that simultaneously block the two pockets. However, no attempt has been successful. In the present study, we synthesized pterin-7-carboxamides with tripeptide pendants and found that one of them interacts with both pockets simultaneously to exhibit good RTA inhibitory activity. X-ray crystallographic analysis of the RTA crystal with the new inhibitor revealed that the conformational change of Tyr80 is an important factor that allows the inhibitors to plug the two pockets simultaneously.

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Organizational Affiliation: 
• Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, Japan.
Research Center for Materials with Integrated Properties, Toho University, Funabashi, Chiba, Japan.
Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.75 kDa 
• Atom Count: 2,335 
• Modeled Residue Count: 261 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin A chain	A	274	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JKU (Subject of Investigation/LOI)	B [auth A]	(2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-5-(phenylmethoxycarbonylamino)pentanoic acid C31 H33 N9 O8 QOJLCYQYXRRJPT-SFTDATJTSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.639	α = 90
b = 67.639	β = 90
c = 141.079	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Katakura, S., Goto, M., Ohba, T., Kawata, R., Nagatsu, K., Higashi, S., Matsumoto, K., Kurisu, K., Ohtsuka, K., Saito, R.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP19K05699

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2022-12-21
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description