5C80

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

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 61: 954-973


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: udpDN30_1909VC39_02535VC78_02550VS27_10630WG08_05660
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
URI
Query on URI

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth F]
G [auth A]
L [auth B]
R [auth C]
AA [auth E],
CA [auth F],
G [auth A],
L [auth B],
R [auth C],
V [auth D]
URIDINE
C9 H12 N2 O6
DRTQHJPVMGBUCF-XVFCMESISA-N
TRS
Query on TRS

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BA [auth E]
DA [auth F]
EA [auth F]
FA [auth F]
H [auth A]
BA [auth E],
DA [auth F],
EA [auth F],
FA [auth F],
H [auth A],
M [auth B],
S [auth C],
W [auth D],
X [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B],
T [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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GA [auth F],
N [auth B],
Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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HA [auth F]
J [auth A]
K [auth A]
P [auth B]
U [auth C]
HA [auth F],
J [auth A],
K [auth A],
P [auth B],
U [auth C],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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IA [auth F],
Q [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.255α = 71.81
b = 73.11β = 77.19
c = 83.137γ = 85.69
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

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: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description