5CBX Dna Binding Protein Dna date Jul 01, 2015
title Ancgr Dna Binding Domain - (+)Gre Complex
authors W.H.Hudson, E.A.Ortlund
compound source
Molecule: Ancgr Dna Binding Domain
Chain: A, B, E, F
Synonym: Glucocorticoid Receptor
Engineered: Yes
Organism_scientific: Unclassified
Organism_taxid: 32644
Gene: Nr3c1, Grl
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Cpcpapgpapapcpapgpapgptpgptptpcptpg)-3'
Chain: C, H
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630

Molecule: Dna (5'- D(Tpcpapgpapapcpapcptpcptpgptptpcptpg)-3'
Chain: D, G
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.820 81.575 116.520 90.00 97.19 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B


Primary referenceDistal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space., Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund EA, Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):326-31. doi:, 10.1073/pnas.1518960113. Epub 2015 Dec 29. PMID:26715749
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (5cbx.pdb1.gz) 39 Kb
  • Biological Unit Coordinates (5cbx.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 5CBX
  • CSU: Contacts of Structural Units for 5CBX
  • Structure Factors (976 Kb)
  • Retrieve 5CBX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CBX from S2C, [Save to disk]
  • Re-refined 5cbx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CBX 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 5CBX
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cbx_F] [5cbx_A] [5cbx_H] [5cbx_D] [5cbx_E] [5cbx_B] [5cbx] [5cbx_C] [5cbx_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5CBX: [ZnF_C4 ] by SMART
  • Other resources with information on 5CBX
  • Community annotation for 5CBX at PDBWiki (http://pdbwiki.org)

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