3CO3 Dna date Mar 27, 2008
title X-Ray Crystal Structure Of A Monofunctional Platinum-Dna Add {Pt(Nh3)2(Pyridine)}2+ Bound To Deoxyguanosine In A Dodecam
authors K.S.Lovejoy, R.C.Todd, S.Zhang, M.S.Mccormick, J.A.D'Aquino, J.T. A.Sancar, K.M.Giacomini, S.J.Lippard
compound source
Molecule: 5'-D(Dcpdcpdtpdcpdtpdcpdgpdtpdcpdtpdcp
Chain: A
Engineered: Yes
 Synthetic: Yes

Molecule: 5'-D(Dgpdgpdapdgpdapdcpdgpdapdgpdapdgp
Chain: B
Engineered: Yes
Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.225 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.440 66.010 56.050 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.16 Å
ligand C7P enzyme
Primary referencecis-Diammine(pyridine)chloroplatinum(II), a monofunctional platinum(II) antitumor agent: Uptake, structure, function, and prospects., Lovejoy KS, Todd RC, Zhang S, McCormick MS, D'Aquino JA, Reardon JT, Sancar A, Giacomini KM, Lippard SJ, Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8902-7. Epub 2008 Jun 25. PMID:18579768
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (15 Kb) [Save to disk]
  • Biological Unit Coordinates (3co3.pdb1.gz) 11 Kb
  • LPC: Ligand-Protein Contacts for 3CO3
  • CSU: Contacts of Structural Units for 3CO3
  • Likely Quarternary Molecular Structure file(s) for 3CO3
  • Structure Factors (95 Kb)
  • Retrieve 3CO3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CO3 from S2C, [Save to disk]
  • Re-refined 3co3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3CO3 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 3CO3
  • 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 3CO3, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3co3_A] [3co3_B] [3co3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3CO3
  • Community annotation for 3CO3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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