2XNZ

xpt-pbuX C74U Riboswitch from B. subtilis bound to acetoguanamine identified by virtual screening

• PDB DOI: https://doi.org/10.2210/pdb2XNZ/pdb
• NAKB: 2XNZ

• Classification: RNA
• Organism(s): Bacillus subtilis
• Mutation(s): No 


• Deposited: 2010-08-06 Released: 2011-04-06 
• Deposition Author(s): Daldrop, P., Reyes, F.E., Robinson, D.A., Hammond, C.M., Lilley, D.M.J., Batey, R.T., Brenk, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.234 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Novel ligands for a purine riboswitch discovered by RNA-ligand docking.

Daldrop, P., Reyes, F.E., Robinson, D.A., Hammond, C.M., Lilley, D.M., Batey, R.T., Brenk, R.

(2011) Chem Biol 18: 324-335

• PubMed: 21439477 
• DOI: https://doi.org/10.1016/j.chembiol.2010.12.020
• Primary Citation of Related Structures:  
  2XNW, 2XNZ, 2XO0, 2XO1


• PubMed Abstract: 
  

  The increasing number of RNA crystal structures enables a structure-based approach to the discovery of new RNA-binding ligands. To develop the poorly explored area of RNA-ligand docking, we have conducted a virtual screening exercise for a purine riboswitch to probe the strengths and weaknesses of RNA-ligand docking. Using a standard protein-ligand docking program with only minor modifications, four new ligands with binding affinities in the micromolar range were identified, including two compounds based on molecular scaffolds not resembling known ligands. RNA-ligand docking performed comparably to protein-ligand docking indicating that this approach is a promising option to explore the wealth of RNA structures for structure-based ligand design.

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Organizational Affiliation: 

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 22.89 kDa 
• Atom Count: 1,659 
• Modelled Residue Count: 65 
• Deposited Residue Count: 67 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Guanine riboswitch	A	67	Bacillus subtilis

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
3AW	I [auth A]	6-METHYL-1,3,5-TRIAZINE-2,4-DIAMINE C4 H7 N5 NJYZCEFQAIUHSD-UHFFFAOYSA-N
ACT	H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
K	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3AW	PDBBind:  2XNZ	Kd: 1.10e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.234 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.165	α = 90
b = 35.068	β = 90.06
c = 41.798	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Daldrop, P., Reyes, F.E., Robinson, D.A., Hammond, C.M., Lilley, D.M.J., Batey, R.T., Brenk, R.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-06-06
  Changes: Advisory, Data collection, Database references, Structure summary
• Version 1.4: 2023-12-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description