4I9L Crystal structure of the D714A mutant of RB69 DNA polymerase date 2012-12-05
authors Jacewicz, A., Trzemecka, A., Guja, K.E., Plochocka, D., Yakubovskaya, E., Bebenek, A., Garcia-Diaz, M.
compound source
symmetry
R_factor
R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.60
ligand CL, GMP, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


    • Primary referenceA Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site., Jacewicz A, Trzemecka A, Guja KE, Plochocka D, Yakubovskaya E, Bebenek A, Garcia-Diaz M, PLoS One. 2013 Oct 7;8(10):e76700. doi: 10.1371/journal.pone.0076700. PMID:24116139
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (157 Kb) [Save to disk]
  • Biological Unit Coordinates (4i9l.pdb1.gz) 152 Kb
  • LPC: Ligand-Protein Contacts for 4I9L
  • CSU: Contacts of Structural Units for 4I9L
  • Structure Factors (486 Kb)
  • Retrieve 4I9L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4I9L from S2C, [Save to disk]
  • Re-refined 4i9l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4I9L 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 4I9L
  • 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 4I9L, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4i9l_A] [4i9l]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4I9L: [POLBc ] by SMART
    • Other resources with information on 4I9L
  • Community annotation for 4I9L at PDBWiki (http://pdbwiki.org)

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