4HQI Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex date
authors Kowal, E.A., Lad, R., Pallan, P.S., Muffly, E., Wawrzak, Z., Egli, M., Sturla, S.J., Stone, M.P.
compound source
symmetry
R_factor
R_Free 0.29823
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.70
ligand BZG, D3N, SPM, SR enzyme
Primary referenceRecognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction., Kowal EA, Lad RR, Pallan PS, Dhummakupt E, Wawrzak Z, Egli M, Sturla SJ, Stone MP, Nucleic Acids Res. 2013 Jun 8. PMID:23748954
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (17 Kb) [Save to disk]
  • Biological Unit Coordinates (4hqi.pdb1.gz) 12 Kb
  • LPC: Ligand-Protein Contacts for 4HQI
  • CSU: Contacts of Structural Units for 4HQI
  • Structure Factors (53 Kb)
  • Retrieve 4HQI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4HQI from S2C, [Save to disk]
  • Re-refined 4hqi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4HQI 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 4HQI
  • 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 4HQI, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4hqi_B] [4hqi_A] [4hqi]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4HQI
  • Community annotation for 4HQI at PDBWiki (http://pdbwiki.org)

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