5E6D Dna Binding Protein Dna date Oct 09, 2015
title Glucocorticoid Receptor Dna Binding Domain - Icam1 Nf-Kb Res Element Complex
authors W.H.Hudson, E.A.Rye, A.G.Herbst, E.A.Ortlund
compound source
Molecule: Dna (5'-D(Gpcptpcpcpgpgpapaptptptpcp 3');
Chain: C
Fragment: Unp Residues 391-480
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Glucocorticoid Receptor
Chain: A, B
Synonym: Gr,Nuclear Receptor Subfamily 3 Group C Member 1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr3c1, Grl
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3) Plyss
symmetry Space Group: P 21 21 21
R_factor 0.257 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
39.059 97.145 104.018 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ZN enzyme
A, B

Primary referenceCryptic glucocorticoid receptor-binding sites pervade genomic NF-kappaB response elements., Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund EA, Nat Commun. 2018 Apr 6;9(1):1337. doi: 10.1038/s41467-018-03780-1. PMID:29626214
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (5e6d.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 5E6D
  • CSU: Contacts of Structural Units for 5E6D
  • Structure Factors (264 Kb)
  • Retrieve 5E6D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5E6D from S2C, [Save to disk]
  • Re-refined 5e6d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5E6D 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 5E6D
  • 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 5e6d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e6d_B] [5e6d_C] [5e6d_A] [5e6d_D] [5e6d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5E6D
  • Community annotation for 5E6D at PDBWiki (http://pdbwiki.org)

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