1NNJ Hydrolase date Jan 14, 2003
title Crystal Structure Complex Between The Lactococcus Lactis Fpg Abasic Site Containing Dna
authors L.Serre, K.Pereira De Jesus, S.Boiteux, C.Zelwer, B.Castaing
compound source
Molecule: 5'-D(Cptpcptptptp(Pdi)Ptptptpcptpcp
Chain: D
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

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

Organism_scientific: Lactococcus Lactis
Organism_taxid: 1358
Gene: Mutm
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 0.215 R_Free 0.236
length a length b length c angle alpha angle beta angle gamma
92.150 92.150 142.530 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand GOL, PDI, ZN enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1PJI, 1PM5

Primary referenceStructural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA., Pereira de Jesus K, Serre L, Zelwer C, Castaing B, Nucleic Acids Res. 2005 Oct 20;33(18):5936-44. Print 2005. PMID:16243784
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1nnj.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 1NNJ
  • CSU: Contacts of Structural Units for 1NNJ
  • Likely Quarternary Molecular Structure file(s) for 1NNJ
  • Structure Factors (406 Kb)
  • Retrieve 1NNJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NNJ from S2C, [Save to disk]
  • Re-refined 1nnj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1NNJ 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 1NNJ
  • 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 1NNJ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nnja2, region A:1-131 [Jmol] [rasmolscript] [script source]
        - Domain d1nnja1, region A:132-219 [Jmol] [rasmolscript] [script source]
        - Domain d1nnja3, region A:224-271 [Jmol] [rasmolscript] [script source]
  • Fold representative 1nnj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1nnj_E] [1nnj_A] [1nnj] [1nnj_D]
  • SWISS-PROT database: [P42371]
  • Domain organization of [FPG_LACLC] by SWISSPFAM
  • Domains found in 1NNJ: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 1NNJ
  • Community annotation for 1NNJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science