2OXM Hydrolase Dna date Feb 20, 2007
title Crystal Structure Of A Ung2modified Dna Complex That Repres Stabilized Short-Lived Extrahelical State In Ezymatic Dna B Flipping
authors M.A.Bianchet, D.J.Krosky, J.T.Stivers, L.M.Amzel
compound source
Molecule: Dna (5'-D(Tpgptptpaptpcptpt)-3')
Chain: B
Synonym: Udg
Ec: 3.2.2.-
Engineered: Yes
Synthetic: Yes
Other_details: Synthetically Made

Molecule: Dna (5'-D(Apapapgpaptp(4mf)Papcpa)-3')
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetically Made

Molecule: Uracil-Dna Glycosylase
Chain: A
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ung, Dgu, Ung1, Ung15
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.254 R_Free 0.328
length a length b length c angle alpha angle beta angle gamma
48.467 65.567 98.472 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 4MF enzyme Hydrolase E.C.3.2.2 BRENDA

Primary referenceEnzymatic capture of an extrahelical thymine in the search for uracil in DNA., Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel LM, Stivers JT, Nature. 2007 Sep 27;449(7161):433-7. Epub 2007 Aug 19. PMID:17704764
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (2oxm.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 2OXM
  • CSU: Contacts of Structural Units for 2OXM
  • Likely Quarternary Molecular Structure file(s) for 2OXM
  • Structure Factors (88 Kb)
  • Retrieve 2OXM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OXM from S2C, [Save to disk]
  • Re-refined 2oxm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OXM 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 2OXM
  • 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 2OXM, from MSDmotif at EBI
  • Fold representative 2oxm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2oxm] [2oxm_C] [2oxm_B] [2oxm_A]
  • SWISS-PROT database: [P13051]
  • Domain organization of [UNG_HUMAN] by SWISSPFAM
  • Domains found in 2OXM: [UDG] [UreE_C ] by SMART
  • Other resources with information on 2OXM
  • Community annotation for 2OXM 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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