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
crystal
cell
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
Gene
Ontology
ChainFunctionProcessComponent
A


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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