1Y1S Transferase date Nov 19, 2004
title Crystal Structure Of The Uridine Phosphorylase From Salmonel Typhimurium In Complex With Uracil And Sulfate Ion At 2.55a Resolution
authors A.G.Gabdoulkhakov, M.V.Dontsova, G.S.Kachalova, C.Betzel, S.E.Ea A.M.Mikhailov
compound source
Molecule: Uridine Phosphorylase
Chain: A, C, D, F, E, B
Synonym: Urdpase, Upase
Ec: 2.4.2.3
Engineered: Yes
Organism_scientific: Salmonella Typhimurium Lt2
Organism_taxid: 99287
Strain: Lt2
Gene: Udp
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbluescript Iisk
symmetry Space Group: P 21 21 21
R_factor 0.189 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.990 124.120 133.830 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand SO4, URA enzyme Transferase E.C.2.4.2.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (236 Kb) [Save to disk]
  • Biological Unit Coordinates (1y1s.pdb1.gz) 230 Kb
  • LPC: Ligand-Protein Contacts for 1Y1S
  • CSU: Contacts of Structural Units for 1Y1S
  • Likely Quarternary Molecular Structure file(s) for 1Y1S
  • Structure Factors (489 Kb)
  • Retrieve 1Y1S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y1S from S2C, [Save to disk]
  • Re-refined 1y1s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y1S 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 1Y1S
  • 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 1Y1S, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y1s_B] [1y1s_D] [1y1s_A] [1y1s_E] [1y1s_F] [1y1s] [1y1s_C]
  • SWISS-PROT database: [P0A1F6]
  • Domain organization of [UDP_SALTY] by SWISSPFAM
  • Other resources with information on 1Y1S
  • Community annotation for 1Y1S 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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