4U2K

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with anticancer compound at 2.13 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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 new anticancer compound at 1.17 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: 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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M5F
Query on M5F

Download Ideal Coordinates CCD File 
O [auth D],
U [auth F]
1-[(2S)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione
C7 H11 F N4 O2
ZBKWVMMCABYTAU-BYPYZUCNSA-N
4WR
Query on 4WR

Download Ideal Coordinates CCD File 
J [auth B],
P [auth D]
1-[(2R)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione
C7 H11 F N4 O2
ZBKWVMMCABYTAU-SCSAIBSYSA-N
TRS
Query on TRS

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T [auth F]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

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

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M [auth D],
Q [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth B]
K [auth C]
L [auth C]
G [auth A],
H [auth A],
I [auth B],
K [auth C],
L [auth C],
R [auth E],
S [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.28α = 90
b = 91.28β = 90
c = 137.227γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description