4DFM Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dCTP date 2012-01-24
authors Bergen, K., Steck, A., Struett, S., Baccaro, A., Welte, W., Diederichs, K., Marx, A.
compound source
symmetry
R_factor
R_Free 0.2162
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.89
ligand 0L6, DDG, EDO, FMT, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates., Bergen K, Steck AL, Strutt S, Baccaro A, Welte W, Diederichs K, Marx A, J Am Chem Soc. 2012 Apr 11. PMID:22475415
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (197 Kb) [Save to disk]
  • Biological Unit Coordinates (4dfm.pdb1.gz) 190 Kb
  • LPC: Ligand-Protein Contacts for 4DFM
  • CSU: Contacts of Structural Units for 4DFM
  • Structure Factors (447 Kb)
  • Retrieve 4DFM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DFM from S2C, [Save to disk]
  • Re-refined 4dfm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DFM 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 4DFM
  • 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 4DFM, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dfm] [4dfm_A] [4dfm_C] [4dfm_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DFM: [POLAc ] by SMART
    • Other resources with information on 4DFM
  • Community annotation for 4DFM at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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