2OYT Hydrolase Dna date Feb 22, 2007
title Crystal Structure Of Ung2dna(Tm)
authors M.A.Bianchet, D.J.Krosky, J.T.Stivers, L.M.Amzel
compound source
Molecule: Uracil-Dna Glycosylase
Chain: A
Synonym: Udg
Ec: 3.2.2.-
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

Molecule: Dna Strand1
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: Dna Strand2
Chain: C
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.192 R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
48.499 66.318 100.316 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 4MF, AAB 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] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (2oyt.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 2OYT
  • CSU: Contacts of Structural Units for 2OYT
  • Likely Quarternary Molecular Structure file(s) for 2OYT
  • Structure Factors (255 Kb)
  • Retrieve 2OYT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OYT from S2C, [Save to disk]
  • Re-refined 2oyt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OYT 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 2OYT
  • 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 2OYT, from MSDmotif at EBI
  • Fold representative 2oyt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2oyt_B] [2oyt_A] [2oyt_C] [2oyt]
  • SWISS-PROT database: [P13051]
  • Domain organization of [UNG_HUMAN] by SWISSPFAM
  • Domains found in 2OYT: [UDG] [UreE_C ] by SMART
  • Other resources with information on 2OYT
  • Community annotation for 2OYT 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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