4PDI Crystal structure of a complex between an inhibited LlFpg and a N7-Benzyl-Fapy-dG containing DNA date
authors Coste, F., Castaing, B.
compound source
symmetry
R_factor
R_Free 0.1902
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.10
ligand 2ON, SOS enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceZinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization., Biela A, Coste F, Culard F, Guerin M, Goffinont S, Gasteiger K, Ciesla J, Winczura A, Kazimierczuk Z, Gasparutto D, Carell T, Tudek B, Castaing B, Nucleic Acids Res. 2014;42(16):10748-61. doi: 10.1093/nar/gku613. Epub 2014 Aug, 20. PMID:25143530
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (4pdi.pdb1.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 4PDI
  • CSU: Contacts of Structural Units for 4PDI
  • Structure Factors (1933 Kb)
  • Retrieve 4PDI in mmCIF format [Save to disk]
  • Re-refined 4pdi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4PDI 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 4PDI
  • 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 4PDI, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4pdi_B] [4pdi_C] [4pdi_A] [4pdi]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4PDI: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 4PDI
  • Community annotation for 4PDI at PDBWiki (http://pdbwiki.org)

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