Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.32 kDa 
• Atom Count: 2157 
• Residue Count: 258 
• Unique protein chains: 1

2R3D

Ricin A-chain (recombinant) complex with Acetamide

• DOI: 10.2210/pdb2R3D/pdb
• Entry: 2R3D supersedes: 1ZB2

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


• Deposited: 2007-08-29 Released: 2007-11-20 
• Deposition Author(s): Carra, J.H., McHugh, C.A., Mulligan, S., Machiesky, L.M., Soares, A.S., Millard, C.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.272 
• R-Value Work: 0.234 

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

• PubMed: 17986339 
• DOI: 10.1186/1472-6807-7-72
• Primary Citation of Related Structures:  
  2R3D, 2R2X, 2P8N, 2PJO


• 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 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.

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Organizational Affiliation: 

United States Army Medical Research Institute of Infectious Diseases, 1425 Porter St,, Fort Detrick, MD 21702, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin A chain (EC 3.2.2.22)	A	268	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
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
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACM	A	ACETAMIDE C2 H5 N O DLFVBJFMPXGRIB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ACM	Kd:  1400000000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.272 
• R-Value Work: 0.234 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.11	α = 90
b = 67.11	β = 90
c = 141.32	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction
LSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-29 
• Released Date: 2007-11-20 
Deposition Author(s): Carra, J.H., McHugh, C.A., Mulligan, S., Machiesky, L.M., Soares, A.S., Millard, C.B.
• This entry supersedes: 1ZB2

Revision History 

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description