4OGK

X-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

X-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution

Sotnichenko, S.E.Lashkov, A.A.Gabdoulkhakov, A.G.Mikhailov, A.M.

To be published.

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 Typhimurium str. LT2Mutation(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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
THM
Query on THM

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
L [auth D],
N [auth E],
Q [auth F]
THYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
O [auth E]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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M [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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I [auth A],
K [auth C],
P [auth E],
S [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
H [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
R [auth F]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.97α = 90
b = 89.97β = 90
c = 256.56γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description