6OD3 Transcription Dna date Mar 25, 2019
title Human Tcf4 C-Terminal Bhlh Domain In Complex With 13-Bp Oligonucleotide Containing E-Box Sequence
authors J.R.Horton, X.Cheng, J.Yang
compound source
Molecule: Transcription Factor 4
Chain: A, B, E, F, G, H, I, J
Fragment: C-Terminal Bhlh Domain (Unp Residues 405-464)
Synonym: Tcf-4, Class B Basic Helix-Loop-Helix Protein 19, Immunoglobulin Transcription Factor 2, Itf-2, Sl3-3 Enhance 2, Sef-2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tcf4, Bhlhb19, Itf2, Sef2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21-Codon Plus(De3)-Ril

Molecule: Dna (5'-D(Cpaptpapcpapcpgptpgptpapt)
Chain: X, W, Y, Z
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor 0.221 R_Free 0.237
length a length b length c angle alpha angle beta angle gamma
47.180 58.946 62.720 104.63 90.34 94.86
method X-Ray Diffractionresolution 1.49 Å
ligand CL, EDO, PG4 enzyme
H, F, A, J, I, G, E, B

Primary referenceStructural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine., Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X, Nucleic Acids Res. 2019 May 13. pii: 5488531. doi: 10.1093/nar/gkz381. PMID:31081034
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (216 Kb) [Save to disk]
  • Biological Unit Coordinates (6od3.pdb1.gz) 68 Kb
  • Biological Unit Coordinates (6od3.pdb2.gz) 67 Kb
  • Biological Unit Coordinates (6od3.pdb3.gz) 40 Kb
  • Biological Unit Coordinates (6od3.pdb4.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 6OD3
  • CSU: Contacts of Structural Units for 6OD3
  • Structure Factors (2580 Kb)
  • Retrieve 6OD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6OD3 from S2C, [Save to disk]
  • View 6OD3 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 6OD3
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6od3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6od3_J] [6od3_I] [6od3_G] [6od3_X] [6od3_E] [6od3_A] [6od3_B] [6od3_Z] [6od3_Y] [6od3_H] [6od3_W] [6od3_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6OD3
  • Community annotation for 6OD3 at PDBWiki (http://pdbwiki.org)

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