4M9E

Structure of Klf4 zinc finger DNA binding domain in complex with methylated DNA

Structural Biology Knowledgebase: 4M9E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 4M9E

Classification: TRANSCRIPTION / DNA

Total Structure Weight: 16896.24


Macromolecule Entities
Molecule Chains Length Organism Details
Krueppel-like factor 4 A 88 Mus musculus Fragment: UNP residues 396-483
Gene Name(s): Klf4 Ezf Gklf Zie
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3') B 10 synthetic
DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3') C 10 synthetic

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5CM
Query on 5CM
B, C DNA LINKING C10 H16 N3 O7 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.187
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.71 α = 90.00
b = 48.71 β = 90.00
c = 131.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-08-14
  • Released Date: 2014-02-12
  • Deposition author(s): Liu, Y., Olanrewaju, Y.O., Blumenthal, R.M., Zhang, X., Cheng, X.

Revision History

  • 2014-05-21
    Type: Citation | Details: Citation update
  • 2014-03-19
    Type: Citation | Details: Citation update