5L06 Dna date Jul 26, 2016
title Solution Structure Of A Dna Dodecamer With 5-Methylcytosine Position
authors H.L.Miears, J.J.Hoppins, D.R.Gruber, R.D.Kasymov, D.O.Zharkov, S.
compound source
Molecule: Dna (5'-D(Cpgp(5cm)Pgpapaptptpcpgpcpg
Chain: A, B
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
methodSolution NMR
ligand 5CM enzyme
Primary referenceOxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation., Gruber DR, Toner JJ, Miears HL, Shernyukov AV, Kiryutin AS, Lomzov AA, Endutkin AV, Grin IR, Petrova DV, Kupryushkin MS, Yurkovskaya AV, Johnson EC, Okon M, Bagryanskaya EG, Zharkov DO, Smirnov SL, Nucleic Acids Res. 2018 Nov 16;46(20):10827-10839. doi: 10.1093/nar/gky893. PMID:30289469
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (119 Kb) [Save to disk]
  • Biological Unit Coordinates (5l06.pdb1.gz) 14 Kb
  • LPC: Ligand-Protein Contacts for 5L06
  • CSU: Contacts of Structural Units for 5L06
  • Original NMR restraints for 5L06 from PDB
  • Retrieve 5L06 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L06 from S2C, [Save to disk]
    • View 5L06 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.
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    • Visual 3D analysis of 5L06
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5l06] [5l06_B] [5l06_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5L06
  • Community annotation for 5L06 at PDBWiki (http://pdbwiki.org)

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