1DPL Dna date Dec 27, 1999
title A-Dna Decamer Gcgta(T23)Tacgc With Incorporated 2'-Methoxy-3 Methylenephosphate-Thymidine
authors M.Egli, V.Tereshko, M.Teplova, G.Minasov, A.Joachimiak, R.Sanishv C.M.Weeks, R.Miller, M.A.Maier, H.An, P.Dan Cook, M.Manoharan
compound source
Molecule: 5'-D(Gpcpgptpap(T23)Papcpgpc)-3'
Chain: A, B
Engineered: Yes
 Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
24.627 42.717 46.906 90.00 90.00 90.00
method X-Ray Diffractionresolution 0.83 Å
ligand MG, SPM, T23 enzyme
Primary referenceX-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution., Egli M, Tereshko V, Teplova M, Minasov G, Joachimiak A, Sanishvili R, Weeks CM, Miller R, Maier MA, An H, Dan Cook P, Manoharan M, Biopolymers 1998;48(4):234-52. PMID:10699842
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (1dpl.pdb1.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 1DPL
  • CSU: Contacts of Structural Units for 1DPL
  • Likely Quarternary Molecular Structure file(s) for 1DPL
  • Structure Factors (376 Kb)
  • Retrieve 1DPL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DPL from S2C, [Save to disk]
  • Re-refined 1dpl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1DPL 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 1DPL
  • 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 1DPL, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dpl_B] [1dpl] [1dpl_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 1DPL
  • Community annotation for 1DPL 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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