4PDI Hydrolase Dna date Apr 18, 2014
title Crystal Structure Of A Complex Between An Inhibited Llfpg An Benzyl-Fapy-Dg Containing Dna
authors F.Coste, B.Castaing
compound source
Molecule: Formamidopyrimidine-Dna Glycosylase
Chain: A
Synonym: Fapy-Dna Glycosylase,Dna-(Apurinic Or Apyrimidinic Lyase Mutm,Ap Lyase Mutm;
Ec: 3.2.2.23
Engineered: Yes
Organism_scientific: Lactococcus Lactis Subsp. Cremoris
Organism_taxid: 1359
Gene: Mutm, Fpg
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Cptpcptptptp(Sos)Ptptptpcpt 3');
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcpgpapgpapapapcpapapapgp
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.160 R_Free 0.190
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.535 91.535 140.974 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 2ON, SOS enzyme Hydrolase E.C.3.2.2.23 BRENDA
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
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4PDI, from MSDmotif at EBI
  • Fold representative 4pdi from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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