1ODG Hydrolase date Feb 19, 2003
title Very-Short-Patch Dna Repair Endonuclease Bound To Its Reaction Product Site
authors K.A.Bunting, S.M.Roe, A.Headley, T.Brown, R.Savva, L.H.Pearl
compound source
Molecule: Dna Mismatch Endonuclease
Chain: A
Synonym: Very Short Patch Repair Protein, Vsr Mismatch Endonuclease, V.Ecokdcm, Vsr, B1960;
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834 (De3)
Expression_system_plasmid: Pet28

Molecule: 5'-D(Tpapgpgpcp5cmtpgpgpaptpcp)-3'
Chain: F, W

Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 61
R_factor 0.2873 R_Free 0.3561
length a length b length c angle alpha angle beta angle gamma
102.805 102.805 64.290 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.8 Å
ligand 5CM, ZN enzyme
related structures by homologous chain: 1CW0

Primary referenceCrystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix., Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH, Nucleic Acids Res 2003 Mar 15;31(6):1633-9. PMID:12626704
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (1odg.pdb1.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 1ODG
  • CSU: Contacts of Structural Units for 1ODG
  • Likely Quarternary Molecular Structure file(s) for 1ODG
  • Structure Factors (67 Kb)
  • Retrieve 1ODG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ODG from S2C, [Save to disk]
  • Re-refined 1odg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1ODG 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 1ODG
  • 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 1ODG, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1odga_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1odg 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: [1odg_F] [1odg_A] [1odg_W] [1odg]
  • SWISS-PROT database: [P09184]
  • Domain organization of [VSR_ECOLI] by SWISSPFAM
  • Other resources with information on 1ODG
  • Community annotation for 1ODG 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