1WV5 Dna date Dec 11, 2004
title X-Ray Structure Of The A-Decamer Gcgtatacgc With A Single 2' Thymine In Place Of T6, Mg-Form
authors M.Egli, G.Minasov, V.Tereshko, P.S.Pallan, M.Teplova, G.B.Inamati E.A.Lesnik, S.R.Owens, B.S.Ross, T.P.Prakash, M.Manoharam
compound source
Molecule: 5'-D(Gpcpgptpap(2bt)Papcpgpc)-3'
Chain: A, B
Engineered: Yes
 Synthetic: Yes
symmetry Space Group: P 41 21 2
R_factor 0.237 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.435 44.434 69.533 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 2BT, MG 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):9045-57. PMID:15966728
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (14 Kb) [Save to disk]
  • Biological Unit Coordinates (1wv5.pdb1.gz) 9 Kb
  • LPC: Ligand-Protein Contacts for 1WV5
  • CSU: Contacts of Structural Units for 1WV5
  • Likely Quarternary Molecular Structure file(s) for 1WV5
  • Structure Factors (22 Kb)
  • Retrieve 1WV5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1WV5 from S2C, [Save to disk]
  • Re-refined 1wv5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1WV5 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 1WV5
  • 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 1WV5, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1wv5_A] [1wv5_B] [1wv5]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 1WV5
  • Community annotation for 1WV5 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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