5EPU

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.105 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A.

Prokofev, I.I.Lashkov, A.A.Gabdoulkhakov, A.G.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
NA
Query on NA

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A, C, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CYT
Query on CYT

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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
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

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A, B, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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B, F
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.105 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 92.848α = 90.00
b = 96.715β = 119.96
c = 92.890γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RFBRRussian Federation14-04-00952a

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release