1Y9F Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-allyl Thymidine (T*) date
authors Egli, M., Minasov, G., Tereshko, V., Pallan, P.S., Teplova, M., Inamati, G.B., Lesnik, E.A., Owens, S.R., Ross, B.S., Prakash, T.P., Manoharan, M.
compound source
symmetry
R_factor
R_Free 0.1852
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.60
ligand 2AT enzyme
Primary referenceProbing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications(,)., Egli M, Minasov G, Tereshko V, Pallan PS, Teplova M, Inamati GB, Lesnik EA, Owens SR, Ross BS, Prakash TP, Manoharan M, Biochemistry 2005 Jun 28;44(25):9045-9057. PMID:15966728
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (15 Kb) [Save to disk]
  • Biological Unit Coordinates (1y9f.pdb1.gz) 11 Kb
  • LPC: Ligand-Protein Contacts for 1Y9F
  • CSU: Contacts of Structural Units for 1Y9F
  • Likely Quarternary Molecular Structure file(s) for 1Y9F
  • Structure Factors (52 Kb)
  • Retrieve 1Y9F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y9F from S2C, [Save to disk]
  • Re-refined 1y9f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1Y9F 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 1Y9F
  • 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 1Y9F, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y9f] [1y9f_A] [1y9f_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 1Y9F
  • Community annotation for 1Y9F at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science