1RXU Transferase date Dec 18, 2003
title E. Coli Uridine Phosphorylase: Thymidine Phosphate Complex
authors T.T.Caradoc-Davies, S.M.Cutfield, I.L.Lamont, J.F.Cutfield
compound source
Molecule: Uridine Phosphorylase
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Synonym: Urdpase, Upase
Ec: 2.4.2.3
Engineered: Yes
Other_details: This Structure Consists Of Eighteen Monomers Which Are In The Closed Conformation Containing Substrate ( And Phosphate). Due To The Large Size Of The Model It Was R Using A Template Model, And Shell Scripts Were Written To C 18 Monomer Model From This Input Model Using The Ncs Operat Relating Each Monomer To The Template. The 18 Monomer Model Refined Using Refmac5 And Ncs Restraints Were Applied As A Positional (0.05a) And Loose Thermal (5.0a3) Restraints. Th Restraints, Along With Tls Restraints Where Each Monomer Wa As A Separate Tls Domain, Were Applied With Each Monomer Be Restrained Against The Template Model.
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
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: Pproex::Pvds
symmetry Space Group: P 1 21 1
R_factor 0.212 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
156.244 97.655 161.453 90.00 118.23 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand K, PO4, THM enzyme Transferase E.C.2.4.2.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, N, K, E, Q, M, C, L, A, J, O, P, B, H, D, R, I, G


Primary referenceCrystal structures of Escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium., Caradoc-Davies TT, Cutfield SM, Lamont IL, Cutfield JF, J Mol Biol 2004 Mar 19;337(2):337-54. PMID:15003451
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (709 Kb) [Save to disk]
  • Biological Unit Coordinates (1rxu.pdb1.gz) 238 Kb
  • Biological Unit Coordinates (1rxu.pdb2.gz) 240 Kb
  • Biological Unit Coordinates (1rxu.pdb3.gz) 240 Kb
  • LPC: Ligand-Protein Contacts for 1RXU
  • CSU: Contacts of Structural Units for 1RXU
  • Likely Quarternary Molecular Structure file(s) for 1RXU
  • Structure Factors (647 Kb)
  • Retrieve 1RXU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RXU from S2C, [Save to disk]
  • Re-refined 1rxu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1RXU 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 1RXU
  • 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 1RXU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rxua_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rxub_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1rxuc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1rxud_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1rxue_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1rxuf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1rxug_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1rxuh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1rxui_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1rxuj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1rxuk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1rxul_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1rxum_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1rxun_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1rxuo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1rxup_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1rxuq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1rxur_, region R [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1rxu_Q] [1rxu_P] [1rxu_O] [1rxu_F] [1rxu_D] [1rxu_H] [1rxu_N] [1rxu_L] [1rxu_M] [1rxu] [1rxu_E] [1rxu_C] [1rxu_A] [1rxu_R] [1rxu_I] [1rxu_J] [1rxu_G] [1rxu_B] [1rxu_K]
  • SWISS-PROT database: [P12758]
  • Domain organization of [UDP_ECOLI] by SWISSPFAM
    • Other resources with information on 1RXU
  • Community annotation for 1RXU at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science