4PD2 Crystal structure of a complex between a C248GH LlFpg mutant and a THF containing DNA date
authors Coste, F., Castaing, B.
compound source
symmetry
R_factor
R_Free 0.1789
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.65
ligand 3DR, ZN 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] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (4pd2.pdb1.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 4PD2
  • CSU: Contacts of Structural Units for 4PD2
  • Structure Factors (3830 Kb)
  • Retrieve 4PD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4PD2 from S2C, [Save to disk]
  • Re-refined 4pd2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4PD2 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 4PD2
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4PD2, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4pd2_C] [4pd2] [4pd2_B] [4pd2_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4PD2: [Fapy_DNA_glyco] [H2TH ] by SMART
    • Other resources with information on 4PD2
  • Community annotation for 4PD2 at PDBWiki (http://pdbwiki.org)

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