5EY3

X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.905 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate

Balaev, V.V.Lashkov, A.A.Gabdulkhakov, A.G.Betzel, C.Mikhailov, A.M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidine phosphorylase
A, B
442Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: deoA
EC: 2.4.2.4
Find proteins for Q7CP66 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q7CP66
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CTN
Query on CTN

Download SDF File 
Download CCD File 
B
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
CYTIDINE
C9 H13 N3 O5
UHDGCWIWMRVCDJ-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.905 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 193.398α = 90.00
b = 193.398β = 90.00
c = 58.208γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation14-04-00952

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Advisory, Author supporting evidence