4G8J

X-ray Structure of Uridine Phosphorylease from Vibrio cholerae Complexed with Thymidine at 2.12 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.119 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

X-ray structure of uridine phosphorylease from Vibrio cholerae complexed with thymidine

Lashkov, A.A.Gabdoulkhakov, A.G.Prokofev, I.I.Sotnichenko, S.E.Betzel, C.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
253Vibrio choleraeMutation(s): 0 
Gene Names: udp (udp_1)
EC: 2.4.2.3
Find proteins for Q9K4U1 (Vibrio cholerae)
Go to UniProtKB:  Q9K4U1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
B, C, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
C, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
THM
Query on THM

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Download CCD File 
A, B, C, D, E, F
THYMIDINE
DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.119 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.796α = 90.00
b = 95.905β = 119.96
c = 91.890γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release