2Y1T Hydrolase date Dec 10, 2010
title Bacillus Subtilis Prophage Dutpase In Complex With Dudp
authors J.Garcia-Nafria, M.Harkiolaki, R.Persson, M.J.Fogg, K.S.Wilson
compound source
Molecule: Spbc2 Prophage-Derived Deoxyuridine 5'-Triphospha Nucleotidohydrolase Yoss;
Chain: A, B, C, D, E, F
Synonym: Deoxyuridine Triphosphate Nucleotidohydrolase, Dut Pyrophosphatase;
Ec: 3.6.1.23
Engineered: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
symmetry Space Group: P 21 21 21
R_factor 0.140 R_Free 0.166
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.515 99.338 99.306 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.89 Å
ligand DUD enzyme Hydrolase E.C.3.6.1.23 BRENDA
note 2Y1T is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceThe structure of Bacillus subtilis SPbeta prophage dUTPase and its complexes with two nucleotides., Garcia-Nafria J, Harkiolaki M, Persson R, Fogg MJ, Wilson KS, Acta Crystallogr D Biol Crystallogr. 2011 Mar;67(Pt 3):167-75. Epub 2011, Feb 15. PMID:21358047
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (2y1t.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (2y1t.pdb2.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 2Y1T
  • CSU: Contacts of Structural Units for 2Y1T
  • Structure Factors (3629 Kb)
  • Retrieve 2Y1T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Y1T from S2C, [Save to disk]
  • Re-refined 2y1t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Y1T 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 2Y1T
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2Y1T, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2y1t_A] [2y1t_D] [2y1t_C] [2y1t_E] [2y1t_B] [2y1t_F] [2y1t]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2Y1T
  • Community annotation for 2Y1T 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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