5K5J Transcription Dna date May 23, 2016
title Homo Sapiens Ccctc-Binding Factor (Ctcf) Znf5-8 And Dna Comp Structure In Space Group P41212
authors H.Hashimoto, X.Cheng
compound source
Molecule: Transcriptional Repressor Ctcf
Chain: A
Fragment: Unp Residues 378-489
Synonym: 11-Zinc Finger Protein,Ccctc-Binding Factor,Ctcfl
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ctcf
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-(De3)-Ril Codon Plus
Expression_system_vector_type: Pgex-6p-1
Expression_system_plasmid: Pxc1199

Molecule: Dna (5'-D(Cpcpcptpgpcptpgpgpcpapapc)
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Tptpgpcpcpapgpcpapgpgpgpg)
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.208 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.903 58.903 172.264 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.29 Å
ligand ACT, SO4, ZN enzyme
Primary referenceStructural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA., Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X, Mol Cell. 2017 Jun 1;66(5):711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Epub, 2017 May 18. PMID:28529057
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (5k5j.pdb1.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 5K5J
  • CSU: Contacts of Structural Units for 5K5J
  • Structure Factors (230 Kb)
  • Retrieve 5K5J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K5J from S2C, [Save to disk]
  • Re-refined 5k5j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5K5J in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5K5J
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5k5j_B] [5k5j_A] [5k5j] [5k5j_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5K5J
  • Community annotation for 5K5J at PDBWiki (http://pdbwiki.org)

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