Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 35.52 kDa 
• Atom Count: 2738 
• Modelled Residue Count: 287 
• Deposited Residue Count: 304 
• Unique protein chains: 1

3UBD

Structure of N-terminal domain of RSK2 kinase in complex with flavonoid glycoside SL0101

• PDB DOI: 10.2210/pdb3UBD/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-10-24 Released: 2012-09-05 
• Deposition Author(s): Utepbergenov, D., Derewenda, U., Derewenda, Z.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.223 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Insights into the Inhibition of the p90 Ribosomal S6 Kinase (RSK) by the Flavonol Glycoside SL0101 from the 1.5 A Crystal Structure of the N-Terminal Domain of RSK2 with Bound Inhibitor.

Utepbergenov, D., Derewenda, U., Olekhnovich, N., Szukalska, G., Banerjee, B., Hilinski, M.K., Lannigan, D.A., Stukenberg, P.T., Derewenda, Z.S.

(2012) Biochemistry 51: 6499-6510

• PubMed: 22846040 
• DOI: 10.1021/bi300620c
• Primary Citation of Related Structures:  
  3UBD, 4EL9


• PubMed Abstract: 
  

The p90 ribosomal S6 family of kinases (RSK) are potential drug targets, due to their involvement in cancer and other pathologies. There are currently only two known selective inhibitors of RSK, but the basis for selectivity is not known. One of these inhibitors is a naturally occurring kaempferol-α-L-diacetylrhamnoside, SL0101. Here, we report the crystal structure of the complex of the N-terminal kinase domain of the RSK2 isoform with SL0101 at 1.5 Å resolution. The refined atomic model reveals unprecedented structural reorganization of the protein moiety, as compared to the nucleotide-bound form. The entire N-lobe, the hinge region, and the αD-helix undergo dramatic conformational changes resulting in a rearrangement of the nucleotide binding site with concomitant formation of a highly hydrophobic pocket spatially suited to accommodate SL0101. These unexpected results will be invaluable in further optimization of the SL0101 scaffold as a promising lead for a novel class of kinase inhibitors.

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Organizational Affiliation: 

Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA 22908, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S6 kinase alpha-3	A	304	Mus musculus	Mutation(s): 0  Gene Names: Mapkapk1b, Rps6ka-rs1, Rps6ka3, Rsk2 EC: 2.7.11.1
UniProt
Find proteins for P18654 (Mus musculus) Explore P18654  Go to UniProtKB:  P18654

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SL0	B [auth A]	5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl 3,4-di-O-acetyl-6-deoxy-alpha-L-mannopyranoside C25 H24 O12 SXOZSDJHGMAEGZ-IGKKHSBFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SL0	Binding MOAD:  3UBD	Kd: 2900 (nM) from 1 assay(s)
	PDBBind:  3UBD	Kd: 2900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.223 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.446	α = 90
b = 40.7	β = 114.54
c = 83.354	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-24 
• Released Date: 2012-09-05 
Deposition Author(s): Utepbergenov, D., Derewenda, U., Derewenda, Z.S.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Advisory, Refinement description