5CBY Dna Binding Protein Dna date Jul 01, 2015
title Ancgr2 Dna Binding Domain - (+)Gre Complex
authors W.H.Hudson, E.A.Ortlund
compound source
Molecule: Ancgr2 Dna Binding Domain
Chain: A, B
Synonym: Gr,Nuclear Receptor Subfamily 3 Group C Member 1
Engineered: Yes
Organism_scientific: Unclassified
Organism_taxid: 32644
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.182 R_Free 0.217
length a length b length c angle alpha angle beta angle gamma
131.644 38.798 98.250 90.00 119.65 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ZN enzyme
A, 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] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (5cby.pdb1.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 5CBY
  • CSU: Contacts of Structural Units for 5CBY
  • Structure Factors (476 Kb)
  • Retrieve 5CBY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CBY from S2C, [Save to disk]
  • Re-refined 5cby structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CBY 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 5CBY
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5cby from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cby_D] [5cby_C] [5cby_B] [5cby_A] [5cby]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5CBY: [ZnF_C4 ] by SMART
  • Other resources with information on 5CBY
  • Community annotation for 5CBY at PDBWiki (http://pdbwiki.org)

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