2XZU Hydrolase Dna date Nov 29, 2010
title Crystal Structure Of A Complex Between The Wild-Type Lactoco Lactis Fpg (Mutm) And An Oxidized Pyrimidine Containing Dna
authors Y.V.Lebihan, M.A.Izquierdo, F.Coste, F.Culard, T.H.Gehrke, K.Essa P.Aller, T.Carrel, B.Castaing
compound source
Molecule: Formamidopyrimidine-Dna Glycosylase
Chain: A
Synonym: Fapy-Dna Glycosylase, Dna-(Apurinic Or Apyrimidini Lyase Mutm, Ap Lyase Mutm;
Ec: 3.2.2.23, 4.2.99.18
Engineered: Yes
Other_details: Chain A Residue P 1 Covalently Linked To Cha Residue Vet 7;
Organism_scientific: Lactococcus Lactis
Organism_taxid: 1359
Strain: Subsp Cremoris
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pflag

Molecule: 5'-D(Cptpcptptptpvetptptptpcptpcpg)
Chain: B
Engineered: Yes
Other_details: Chain B Residue Vet 7 Covalently Linked To C Residue P 1;

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Gpcpgpapgpapapapcpapapapga)-3'
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.157 R_Free 0.189
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.739 91.739 143.236 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.82 Å
ligand GOL, VET, ZN enzyme Hydrolase E.C.3.2.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary reference5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases., Le Bihan YV, Angeles Izquierdo M, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carell T, Castaing B, Nucleic Acids Res. 2011 Aug;39(14):6277-90. Epub 2011 Apr 12. PMID:21486746
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (128 Kb) [Save to disk]
  • Biological Unit Coordinates (2xzu.pdb1.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 2XZU
  • CSU: Contacts of Structural Units for 2XZU
  • Structure Factors (405 Kb)
  • Retrieve 2XZU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XZU from S2C, [Save to disk]
  • Re-refined 2xzu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XZU 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 2XZU
  • 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 2XZU, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xzu] [2xzu_B] [2xzu_A] [2xzu_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XZU: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 2XZU
  • Community annotation for 2XZU at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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