3FWP

X-ray structure of uridine nucleoside phosphorylease from Salmonella typhimurium complexed with phosphate and its inhibitor 2,2'-anhydrouridine at 1.86 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The X-ray structure of Salmonella typhimurium uridine nucleoside phosphorylase complexed with 2,2'-anhydrouridine, phosphate and potassium ions at 1.86 A resolution.

Lashkov, A.A.Zhukhlistova, N.E.Gabdoulkhakov, A.H.Shtil, A.A.Efremov, R.G.Betzel, C.Mikhailov, A.M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 51-60

  • DOI: https://doi.org/10.1107/S0907444909044175
  • Primary Citation of Related Structures:  
    3FWP

  • PubMed Abstract: 

    Uridine nucleoside phosphorylase is an important drug target for the development of anti-infective and antitumour agents. The X-ray crystal structure of Salmonella typhimurium uridine nucleoside phosphorylase (StUPh) complexed with its inhibitor 2,2'-anhydrouridine, phosphate and potassium ions has been solved and refined at 1.86 A resolution (R(cryst) = 17.6%, R(free) = 20.6%). The complex of human uridine phosphorylase I (HUPhI) with 2,2'-anhydrouridine was modelled using a computational approach. The model allowed the identification of atomic groups in 2,2'-anhydrouridine that might improve the interaction of future inhibitors with StUPh and HUPhI.


  • Organizational Affiliation

    A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky Prospect, 119333 Moscow, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase
A, B, C, D, E
A, B, C, D, E, F
253Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: STM3968STMD1.21udp
EC: 2.4.2.3
UniProt
Find proteins for P0A1F6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A1F6 
Go to UniProtKB:  P0A1F6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A1F6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANU
Query on ANU

Download Ideal Coordinates CCD File 
I [auth B],
L [auth D],
O [auth F]
2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil
C9 H10 N2 O5
UUGITDASWNOAGG-CCXZUQQUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth B],
K [auth D],
N [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
K
Query on K

Download Ideal Coordinates CCD File 
H [auth B],
J [auth C],
M [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.79α = 90
b = 124.07β = 90
c = 134.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description, Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description