2OEC

Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with 2,2'-anhydrouridine and potassium ion at 2.194A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.194 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with 2,2'-anhydrouridine and potassium ion at 2.194A resolution

Timofeev, V.I.Lashkov, A.A.Pavlyuk, B.P.Gabdoulkhakov, A.G.Kachalova, G.S.Mikhailov, A.M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine phosphorylase
A, B, C, D, E, F
252Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: udp
EC: 2.4.2.3
Find proteins for P0A1F6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P0A1F6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C, E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ANU
Query on ANU

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Download CCD File 
B, F
2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil
Anhydrouridine; 2,2'-ANHYDROURIDINE; CYCLOURIDINE
C9 H10 N2 O5
UUGITDASWNOAGG-CCXZUQQUSA-N
 Ligand Interaction
1PE
Query on 1PE

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Download CCD File 
B, D
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.194 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.520α = 90.00
b = 123.980β = 90.00
c = 133.520γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-18
    Type: Structure summary