3U38 Dna date Oct 05, 2011
title Intercalation Of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccg
authors C.J.Cardin, J.P.Hall, H.Niyazi
compound source
Molecule: 5'-D(Cpcpgpgptpapcpcpgpg)-3'
Chain: A
Engineered: Yes
Synthetic: Yes
Other_details: Oligo Purchased From Atd Bio
symmetry Space Group: P 43 21 2
R_factor 0.176 R_Free 0.232
length a length b length c angle alpha angle beta angle gamma
52.560 52.560 32.430 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.13 Å
ligand BA, RKP enzyme
Primary referenceCrystal structures of Lambda-[Ru(phen)(2)dppz](2)(+) with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes., Niyazi H, Hall JP, O'Sullivan K, Winter G, Sorensen T, Kelly JM, Cardin CJ, Nat Chem. 2012 Jun 24;4(8):621-8. doi: 10.1038/nchem.1397. PMID:22824893
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (13 Kb) [Save to disk]
  • Biological Unit Coordinates (3u38.pdb1.gz) 10 Kb
  • LPC: Ligand-Protein Contacts for 3U38
  • CSU: Contacts of Structural Units for 3U38
  • Structure Factors (38 Kb)
  • Retrieve 3U38 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3U38 from S2C, [Save to disk]
  • Re-refined 3u38 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3U38 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 3U38
  • 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
  • 3D motif for 3U38, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3u38] [3u38_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3U38
  • Community annotation for 3U38 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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