4GUE

Structure of N-terminal kinase domain of RSK2 with flavonoid glycoside quercitrin

Structural Biology Knowledgebase: 4GUE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.171

Literature

Macromolecules
Sequence Display for 4GUE

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 35639.88

Macromolecule Entities
Molecule Chains Length Organism Details
Ribosomal protein S6 kinase alpha-3 A 305 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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo- 4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside
quercitrin (Synonym)
C21 H20 O11
OXGUCUVFOIWWQJ-HQBVPOQASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
QCT N/A in BindingDB
Kd: 5800 nM  BindingMOAD
Kd: 5800 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.171
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 98.08 α = 90.00
b = 40.69 β = 114.31
c = 83.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-29
  • Released Date: 2013-01-30
  • Deposition author(s): Derewenda, U., Utepbergenov, D., Szukalska, G., Derewenda, Z.S.

Revision History

  • 2013-03-27
    Type: Citation | Details: Citation update