4JD8 Racemic-[Ru(phen)2(dppz)]2+] bound to synthetic DNA at high resolution date
authors Cook, D.S., Hall, J.P., Cardin, C.J.
compound source
R_Free 0.162
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.16
ligand 0TN, K, RKP enzyme
note 4JD8 supersedes 4E87
Primary referenceX-ray Crystal Structure of rac-[Ru(phen)2dppz](2+) with d(ATGCAT)2 Shows Enantiomer Orientations and Water Ordering., Hall JP, Cook D, Morte SR, McIntyre P, Buchner K, Beer H, Cardin DJ, Brazier JA, Winter G, Kelly JM, Cardin CJ, J Am Chem Soc. 2013 Aug 28;135(34):12652-9. doi: 10.1021/ja403590e. Epub 2013 Aug, 14. PMID:23875832
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (4jd8.pdb1.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 4JD8
  • CSU: Contacts of Structural Units for 4JD8
  • Structure Factors (227 Kb)
  • Retrieve 4JD8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JD8 from S2C, [Save to disk]
  • Re-refined 4jd8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JD8 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 4JD8
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4JD8, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jd8] [4jd8_A] [4jd8_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4JD8
  • Community annotation for 4JD8 at PDBWiki (http://pdbwiki.org)

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