4LZW

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymidine at 1.29 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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) Crystallogr Rep 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase
A, B, C, D, E
A, B, C, D, E, F
253Vibrio choleraeMutation(s): 0 
Gene Names: udp
EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae)
Explore Q9K4U1 
Go to UniProtKB:  Q9K4U1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K4U1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
THM
Query on THM

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DA [auth E]
G [auth A]
IA [auth F]
N [auth B]
S [auth C]
DA [auth E],
G [auth A],
IA [auth F],
N [auth B],
S [auth C],
Y [auth D]
THYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
EDO
Query on EDO

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EA [auth E],
T [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
EOH
Query on EOH

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FA [auth E]
H [auth A]
I [auth A]
JA [auth F]
O [auth B]
FA [auth E],
H [auth A],
I [auth A],
JA [auth F],
O [auth B],
P [auth B],
Z [auth D]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
CL
Query on CL

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AA [auth D]
GA [auth E]
J [auth A]
KA [auth F]
L [auth A]
AA [auth D],
GA [auth E],
J [auth A],
KA [auth F],
L [auth A],
MA [auth F],
Q [auth B],
U [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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BA [auth D]
CA [auth D]
HA [auth E]
M [auth A]
R [auth B]
BA [auth D],
CA [auth D],
HA [auth E],
M [auth A],
R [auth B],
W [auth C],
X [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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K [auth A],
LA [auth F],
V [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.74α = 90
b = 95.85β = 119.96
c = 91.83γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
XDSdata reduction
MOLREPphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description