4DQQ Ternary complex of Bacillus DNA Polymerase I Large Fragment E658A, DNA duplex, and rCTP (paired with dG of template) in presence of Mg2+ date 2012-02-16
authors Wang, W., Beese, L.S.
compound source
symmetry
R_factor
R_Free 0.1794
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.59
ligand CTP, DOC, MES, MG, MPD, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D


Primary referenceStructural factors that determine selectivity of a high-fidelity DNA polymerase for deoxy-, dideoxy-, and ribo-nucleotides., Wang W, Wu EY, Hellinga HW, Beese LS, J Biol Chem. 2012 May 30. PMID:22648417
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (645 Kb) [Save to disk]
  • Biological Unit Coordinates (4dqq.pdb1.gz) 318 Kb
  • Biological Unit Coordinates (4dqq.pdb2.gz) 321 Kb
  • LPC: Ligand-Protein Contacts for 4DQQ
  • CSU: Contacts of Structural Units for 4DQQ
  • Structure Factors (1420 Kb)
  • Retrieve 4DQQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DQQ from S2C, [Save to disk]
  • Re-refined 4dqq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DQQ 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 4DQQ
  • 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 4DQQ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dqq_D] [4dqq_E] [4dqq_B] [4dqq_C] [4dqq_A] [4dqq] [4dqq_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DQQ: [35EXOc] [POLAc ] by SMART
    • Other resources with information on 4DQQ
  • Community annotation for 4DQQ at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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