2D3Y Hydrolase date Oct 04, 2005
title Crystal Structure Of Uracil-Dna Glycosylase From Thermus The Hb8
authors H.Kosaka, N.Nakagawa, R.Masui, S.Kuramitsu, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Uracil-Dna Glycosylase
Chain: A
Ec: 3.2.2.-
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Ttudgb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 21 21 21
R_factor 0.186 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.180 62.350 63.040 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand ACT, DU, SF4 enzyme Hydrolase E.C.3.2.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of family 5 uracil-DNA glycosylase bound to DNA., Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R, J Mol Biol. 2007 Nov 2;373(4):839-50. Epub 2007 Aug 21. PMID:17870091
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (2d3y.pdb1.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 2D3Y
  • CSU: Contacts of Structural Units for 2D3Y
  • Likely Quarternary Molecular Structure file(s) for 2D3Y
  • Structure Factors (424 Kb)
  • Retrieve 2D3Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D3Y from S2C, [Save to disk]
  • Re-refined 2d3y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D3Y 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 2D3Y
  • 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
  • 3D motif for 2D3Y, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d3y_A] [2d3y]
  • SWISS-PROT database: [Q5SJ65]
  • Domain organization of [Q5SJ65_THET8] by SWISSPFAM
  • Domains found in 2D3Y: [UDG] [UreE_C ] by SMART
  • Other resources with information on 2D3Y
  • Community annotation for 2D3Y 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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