1TDZ Hydrolase Dna date May 24, 2004
title Crystal Structure Complex Between The Lactococcus Lactis Fpg And A Fapy-Dg Containing Dna
authors F.Coste, M.Ober, T.Carell, S.Boiteux, C.Zelwer, B.Castaing
compound source
Molecule: 5'-D(Cptpcptptptp(Fox)Ptptptpcptpcp
Chain: B
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

Molecule: Formamidopyrimidine-Dna Glycosylase
Chain: A
Synonym: Fapy-Dna Glycosylase
Ec: 3.2.2.23
Engineered: Yes

Organism_scientific: Lactococcus Lactis
Organism_taxid: 1358
Gene: Mutm, Fpg
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal-C
symmetry Space Group: P 41 21 2
R_factor 0.179 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.408 91.408 141.575 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand FOX, GOL, ZN enzyme Hydrolase E.C.3.2.2.23 BRENDA
related structures by homologous chain: 1PJJ
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by the Fpg DNA glycosylase., Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B, J Biol Chem 2004 Jul 10;. PMID:15249553
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (1tdz.pdb1.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 1TDZ
  • CSU: Contacts of Structural Units for 1TDZ
  • Likely Quarternary Molecular Structure file(s) for 1TDZ
  • Structure Factors (834 Kb)
  • Retrieve 1TDZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TDZ from S2C, [Save to disk]
  • Re-refined 1tdz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1TDZ 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 1TDZ
  • 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 1TDZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tdza1, region A:132-219 [Jmol] [rasmolscript] [script source]
        - Domain d1tdza2, region A:2-131 [Jmol] [rasmolscript] [script source]
        - Domain d1tdza3, region A:225-271 [Jmol] [rasmolscript] [script source]
  • Fold representative 1tdz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1tdz_A] [1tdz_C] [1tdz] [1tdz_B]
  • SWISS-PROT database: [P42371]
  • Domain organization of [FPG_LACLC] by SWISSPFAM
  • Domains found in 1TDZ: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 1TDZ
  • Community annotation for 1TDZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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