4J2A RB69 DNA Polymerase L415A Ternary Complex date 2013-02-04
authors Xia, S., Wang, J., Konigsberg, W.H.
compound source
symmetry
R_factor
R_Free 0.21124
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.80
ligand CA, TTP enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


    • Primary referenceAlteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics., Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH, Nucleic Acids Res. 2013 Oct;41(19):9077-89. doi: 10.1093/nar/gkt674. Epub 2013, Aug 5. PMID:23921641
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (340 Kb) [Save to disk]
  • Biological Unit Coordinates (4j2a.pdb1.gz) 334 Kb
  • LPC: Ligand-Protein Contacts for 4J2A
  • CSU: Contacts of Structural Units for 4J2A
  • Structure Factors (1558 Kb)
  • Retrieve 4J2A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4J2A from S2C, [Save to disk]
  • Re-refined 4j2a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4J2A 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 4J2A
  • 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 4J2A, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4j2a_A] [4j2a] [4j2a_T] [4j2a_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4J2A: [POLBc ] by SMART
    • Other resources with information on 4J2A
  • Community annotation for 4J2A at PDBWiki (http://pdbwiki.org)

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