5CC1 Dna Binding Protein Dna date Jul 01, 2015
title S425g Glucocorticoid Receptor Dna Binding Domain - (+)Gre Co
authors W.H.Hudson, E.A.Weikum, E.A.Ortlund
compound source
Molecule: Glucocorticoid Receptor
Chain: A, B, W, X
Synonym: Gr,Nuclear Receptor Subfamily 3 Group C Member 1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr3c1, Grl
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.245 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
176.721 39.122 132.099 90.00 101.10 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, W, X, 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] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (5cc1.pdb1.gz) 39 Kb
  • Biological Unit Coordinates (5cc1.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 5CC1
  • CSU: Contacts of Structural Units for 5CC1
  • Structure Factors (634 Kb)
  • Retrieve 5CC1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CC1 from S2C, [Save to disk]
  • Re-refined 5cc1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CC1 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 5CC1
  • 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 5cc1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cc1_D] [5cc1_Z] [5cc1_A] [5cc1_W] [5cc1_C] [5cc1] [5cc1_B] [5cc1_X] [5cc1_Y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5CC1: [ZnF_C4 ] by SMART
  • Other resources with information on 5CC1
  • Community annotation for 5CC1 at PDBWiki (http://pdbwiki.org)

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