5LOK

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.109 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.114 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution

Prokofev, I.I.Gabdoulkhakov, A.G.Lashkov, A.A.Balaev, V.V.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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, C, E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CYT
Query on CYT

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Download CCD File 
A, B, C, D, E, F
6-AMINOPYRIMIDIN-2(1H)-ONE
CYTOSINE
C4 H5 N3 O
OPTASPLRGRRNAP-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B, C, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D, E, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CTN
Query on CTN

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Download CCD File 
A, B, C, D, E, F
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: 1.109 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.114 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 64.258α = 69.35
b = 71.772β = 72.17
c = 89.228γ = 85.78
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RFBRRussian Federation14-04-00952a
Grant of President of Russian FederationRussian FederationMK-9246.2016.3

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release