3UBD

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

Structural Biology Knowledgebase: 3UBD SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3UBD

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 35516.56

Macromolecule Entities
Molecule Chains Length Organism Details
Ribosomal protein S6 kinase alpha-3 A 304 Mus musculus EC#: 2.7.11.1 IUBMB
Fragment: N-terminal kinase domain, UNP residues 45-346
Gene Name(s): Rps6ka3 Mapkapk1b Rps6ka-rs1 Rsk2

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SL0
Query on SL0

A 5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H- chromen-3-yl 3,4-di-O-acetyl-6-deoxy-alpha- L-mannopyranoside
SL 0101-1 (Synonym)
C25 H24 O12
SXOZSDJHGMAEGZ-IGKKHSBFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SL0 N/A in BindingDB
Kd: 2900 nM  BindingMOAD
Kd: 2900 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.193
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 98.45 α = 90.00
b = 40.70 β = 114.54
c = 83.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



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

No revisions since initial release