2P8N

Ricin a-chain (recombinant) complex with adenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

Carra, J.H.McHugh, C.A.Mulligan, S.Machiesky, L.M.Soares, A.S.Millard, C.B.

(2007) BMC Struct.Biol. 7: 72-72

  • DOI: 10.1186/1472-6807-7-72
  • Primary Citation of Related Structures:  2PJN, 2PJO, 2R2X, 2R3D

  • PubMed Abstract: 
  • Ricin is a potent toxin and known bioterrorism threat with no available antidote. The ricin A-chain (RTA) acts enzymatically to cleave a specific adenine base from ribosomal RNA, thereby blocking translation. To understand better the relationship bet ...

    Ricin is a potent toxin and known bioterrorism threat with no available antidote. The ricin A-chain (RTA) acts enzymatically to cleave a specific adenine base from ribosomal RNA, thereby blocking translation. To understand better the relationship between ligand binding and RTA active site conformational change, we used a fragment-based approach to find a minimal set of bonding interactions able to induce rearrangements in critical side-chain positions.


    Organizational Affiliation

    United States Army Medical Research Institute of Infectious Diseases, 1425 Porter St,, Fort Detrick, MD 21702, USA. john.carra@amedd.army.mil




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ricin A chain
A
268Ricinus communisEC: 3.2.2.22
Find proteins for P02879 (Ricinus communis)
Go to UniProtKB:  P02879
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADEKd: 700000 nM BINDINGMOAD
ADEKd: 700000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.265 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.162α = 90.00
b = 68.162β = 90.00
c = 141.195γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance