5EFO

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.63A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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

Prokofev, I.I.Lashkov, A.A.Gabdoulkhakov, A.G.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
253Vibrio 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
CTN
Query on CTN

Download Ideal Coordinates CCD File 
W [auth E],
Z [auth F]
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
C9 H13 N3 O5
UHDGCWIWMRVCDJ-XVFCMESISA-N
TRS
Query on TRS

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I [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CYT
Query on CYT

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H [auth A]
K [auth B]
N [auth C]
O [auth C]
R [auth D]
H [auth A],
K [auth B],
N [auth C],
O [auth C],
R [auth D],
S [auth D]
6-AMINOPYRIMIDIN-2(1H)-ONE
C4 H5 N3 O
OPTASPLRGRRNAP-UHFFFAOYSA-N
PEG
Query on PEG

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M [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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J [auth B],
L [auth C],
T [auth D],
V [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
Q [auth D],
X [auth F],
Y [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
P [auth C],
U [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.949α = 67.54
b = 76.336β = 73.74
c = 89.694γ = 84.92
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



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: 2016-11-09
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description