Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 60.81 kDa 
• Atom Count: 4187 
• Residue Count: 516 
• Unique protein chains: 2

3RTI

Crystal structure of ricin bound with formycin monophosphate

• DOI: 10.2210/pdb3RTI/pdb
• Entry: 3RTI supersedes: 1FMP

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Ricinus communis
• Mutation(s): No 


• Deposited: 2011-05-03 Released: 2011-08-31 
• Deposition Author(s): Monzingo, A.F., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.209 

Literature

X-ray analysis of substrate analogs in the ricin A-chain active site.

Monzingo, A.F., Robertus, J.D.

(1992) J Mol Biol 227: 1136-1145

• PubMed: 1433290 
• DOI: 10.1016/0022-2836(92)90526-p
• Primary Citation of Related Structures:  
  3RTI, 3RTJ


• PubMed Abstract: 
  

Ricin A-chain is an N-glycosidase that hydrolyzes the adenine ring from a specific adenosine of rRNA. Formycin monophosphate (FMP) and adenyl(3'-->5')guanosine (ApG) were bound to ricin A-chain and their structures elucidated by X-ray crystallography. The formycin ring stacks between tyrosines 80 and 123 and at least four hydrogen bonds are made to the adenine moiety. A residue invariant in this enzyme class, Arg180, appears to hydrogen bond to N-3 of the susceptible adenine. Three hypothetical models for binding a true hexanucleotide substrate, CGAGAG, are proposed. They incorporate adenine binding, shown by crystallography, but also include geometry likely to favor catalysis. For example, efforts have been made to orient the ribose ring in a way that allows solvent attack and oxycarbonium stabilization by the enzyme. The favored model is a simple perturbation of the tetraloop structure determined by nuclear magnetic resonance for similar polynucleotides. The model is attractive in that specific roles are defined for conserved protein residues. A mechanism of action is proposed. It invokes oxycarbonium ion stabilization on ribose by Glu177 in the transition state. Arg180 stabilizes anion development on the leaving adenine by protonation at N-3 and may activate a trapped water molecule that is the ultimate nucleophile in the depurination.

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Organizational Affiliation: 

Clayton Foundation Biochemical Institute, Department of Chemistry and Biochemistry, University of Texas, Austin 78712.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin	A	267	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin	B	262	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C, D	2		N/A

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMP	A	FORMYCIN-5'-MONOPHOSPHATE C10 H14 N5 O7 P PBAHXXBYQACZMA-KSYZLYKTSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
FMP	Ki :  43   nM  PDBBind

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	C, D	beta-lactose	Oligosaccharide /  Nutrient		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.74	α = 90
b = 78.49	β = 90
c = 114.34	γ = 90

Software Package:

Software Name	Purpose
San	data collection
X-PLOR	model building
X-PLOR	refinement
San	data reduction
San	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-03 
• Released Date: 2011-08-31 
Deposition Author(s): Monzingo, A.F., Robertus, J.D.
• This entry supersedes: 1FMP

Revision History 

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary