4HV3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1021/jm3016393
  • Primary Citation of Related Structures:  4HUO, 4HUP, 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. T ...

    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.


    Organizational Affiliation

    Department of Chemistry, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan. anslyn@austin.utexas.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ricin
A
268Ricinus communisEC: 3.2.2.22
Find proteins for P02879 (Ricinus communis)
Go to UniProtKB:  P02879
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
19L
Query on 19L

Download SDF File 
Download CCD File 
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
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
A
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
19LIC50: 115000 nM BINDINGMOAD
19LIC50: 115000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.827α = 90.00
b = 67.827β = 90.00
c = 140.673γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
BOSdata collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references
  • Version 1.2: 2015-04-29
    Type: Non-polymer description
  • Version 1.3: 2017-11-15
    Type: Refinement description