4DQI Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and dCTP (paired with dG of template) date 2012-02-15
authors Wang, W., Beese, L.S.
compound source
symmetry
R_factor
R_Free 0.1848
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.69
ligand DCP, DOC, MG, SO4 enzyme
Gene GYMC61
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] (654 Kb) [Save to disk]
  • Biological Unit Coordinates (4dqi.pdb1.gz) 321 Kb
  • Biological Unit Coordinates (4dqi.pdb2.gz) 326 Kb
  • LPC: Ligand-Protein Contacts for 4DQI
  • CSU: Contacts of Structural Units for 4DQI
  • Structure Factors (1142 Kb)
  • Retrieve 4DQI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DQI from S2C, [Save to disk]
  • Re-refined 4dqi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DQI 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 4DQI
  • 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 4DQI, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dqi_E] [4dqi_B] [4dqi_A] [4dqi_F] [4dqi_D] [4dqi_C] [4dqi]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DQI: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 4DQI
  • Community annotation for 4DQI at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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