4IP0

X-Ray Structure of the Complex Uridine Phosphorylase from Vibrio cholerae with Phosphate Ion at 1.29 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.294 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

Prokofev, I.I.Lashkov, A.A.Gabdoulkhakov, A.G.Balaev, V.V.Seregina, T.A.Mironov, A.S.Betzel, C.Mikhailov, A.M.

(2016) Crystallography Reports 61: 954-973


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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D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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B, C, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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A, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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C, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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

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B
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.294 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 63.671α = 69.63
b = 71.062β = 72.56
c = 87.908γ = 85.73
Software Package:
Software NamePurpose
SCALAdata scaling
DNAdata collection
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Database references