5K5J

Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P41212


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 5K5J

Classification: TRANSCRIPTION / DNA

Total Structure Weight: 22084.77


Macromolecule Entities
Molecule Chains Length Organism Details
Transcriptional repressor CTCF A 117 Homo sapiens Fragment: unp residues 378-489
Gene Name(s): CTCF Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*GP*CP*AP*AP*C)-3') B 13 Synthetic construct
DNA (5'-D(*TP*TP*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*G)-3') C 13 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.208
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 58.90 α = 90.00
b = 58.90 β = 90.00
c = 172.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-05-23
  • Released Date: 2017-05-24
  • Deposition author(s): Hashimoto, H., Cheng, X.

Revision History

  • Version 1_0: 2017-05-24

    Type: Initial release

  • Version 1_1: 2017-06-07

    Type: Database references

  • Version 1_2: 2017-06-14

    Type: Database references

  • Version 1_3: 2017-09-20

    Type: Author supporting evidence