5LHV

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine and sulfate ion at 1.29 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.288 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 

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 uridine and sulfate ion at 1.29 A resolution

Prokofev, I.I.Lashkov, A.A.Gabdoulkhakov, A.G.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
251Vibrio 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
SO4
Query on SO4

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A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
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
MG
Query on MG

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

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Download CCD File 
A, B, C, D, E, F
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
URI
Query on URI

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Download CCD File 
A, B, C, D, E, F
URIDINE
C9 H12 N2 O6
DRTQHJPVMGBUCF-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.288 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 64.223α = 69.70
b = 71.648β = 72.70
c = 88.878γ = 86.24
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
PHENIXrefinement

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: 2017-08-02
    Type: Initial release