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: 1.29 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase
A, B, C, D, E
A, B, C, D, E, F
251Vibrio choleraeMutation(s): 0 
Gene Names: 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
URI
Query on URI

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DA [auth D]
I [auth A]
JA [auth E]
Q [auth B]
RA [auth F]
DA [auth D],
I [auth A],
JA [auth E],
Q [auth B],
RA [auth F],
W [auth C]
URIDINE
C9 H12 N2 O6
DRTQHJPVMGBUCF-XVFCMESISA-N
URA
Query on URA

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EA [auth D]
J [auth A]
KA [auth E]
R [auth B]
SA [auth F]
EA [auth D],
J [auth A],
KA [auth E],
R [auth B],
SA [auth F],
X [auth C]
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
SO4
Query on SO4

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CA [auth D]
G [auth A]
H [auth A]
IA [auth E]
O [auth B]
CA [auth D],
G [auth A],
H [auth A],
IA [auth E],
O [auth B],
P [auth B],
QA [auth F],
V [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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BA [auth C]
HA [auth D]
N [auth A]
OA [auth E]
U [auth B]
BA [auth C],
HA [auth D],
N [auth A],
OA [auth E],
U [auth B],
VA [auth F],
WA [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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GA [auth D]
L [auth A]
MA [auth E]
T [auth B]
UA [auth F]
GA [auth D],
L [auth A],
MA [auth E],
T [auth B],
UA [auth F],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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FA [auth D]
K [auth A]
LA [auth E]
PA [auth E]
S [auth B]
FA [auth D],
K [auth A],
LA [auth E],
PA [auth E],
S [auth B],
TA [auth F],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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AA [auth C],
M [auth A],
NA [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.223α = 69.7
b = 71.648β = 72.7
c = 88.878γ = 86.24
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RFBRRussian Federation14-04-00952a

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description