4HV3 | pdb_00004hv3

Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonyl-L-serinyl)-L-tryptophan

• PDB DOI: https://doi.org/10.2210/pdb4HV3/pdb

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


• Deposited: 2012-11-05 Released: 2012-12-26 
• Deposition Author(s): Robertus, J.D., Manzano, L.A., Jasheway, K.R., Monzingo, A.F., Saito, R., Pruet, J.M., Wiget, P.A., Anslyn, E.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Peptide-conjugated pterins as inhibitors of ricin toxin A.

Saito, R., Pruet, J.M., Manzano, L.A., Jasheway, K., Monzingo, A.F., Wiget, P.A., Kamat, I., Anslyn, E.V., Robertus, J.D.

(2013) J Med Chem 56: 320-329

• PubMed: 23214944 
• DOI: https://doi.org/10.1021/jm3016393
• Primary Citation Related Structures: 
  4HUO, 4HUP, 4HV3, 4HV7


• PubMed Abstract: 
  

  Several 7-peptide-substituted pterins were synthesized and tested as competitive active-site inhibitors of ricin toxin A (RTA). Focus began on dipeptide conjugates, and these results further guided the construction of several tripeptide conjugates. The binding of these compounds to RTA was studied via a luminescence-based kinetic assay, as well as through X-ray crystallography. Despite the relatively polar, solvent exposed active site, several hydrophobic interactions, most commonly π-interactions not predicted by modeling programs, were identified in all of the best-performing inhibitors. Nearly all of these compounds provide IC₅₀ values in the low micromolar range.

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Organizational Affiliation: 
• Department of Chemistry, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan. [e-mail]

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: 30.85 kDa 
• Atom Count: 2,397 
• Modeled Residue Count: 268 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin	A	268	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
19L	B [auth A]	(2S)-2-[[(2S)-2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]-3-oxidanyl-propanoyl]amino]-3-(1H-indol-3-yl)propanoic acid C21 H20 N8 O6 PVENGVGTXKBGQJ-JSGCOSHPSA-N
MLA	D [auth A], E [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.827	α = 90
b = 67.827	β = 90
c = 140.673	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Robertus, J.D., Manzano, L.A., Jasheway, K.R., Monzingo, A.F., Saito, R., Pruet, J.M., Wiget, P.A., Anslyn, E.V.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2013-03-06
  Changes: Database references
• Version 1.2: 2015-04-29
  Changes: Non-polymer description
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description