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 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine phosphorylase
A, B, C, D, E, F
253Vibrio choleraeMutation(s): 0 
Gene Names: udp (udp_1)
EC: 2.4.2.3
Find proteins for Q9K4U1 (Vibrio cholerae)
Go to UniProtKB:  Q9K4U1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M5F
Query on M5F

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D, F
1-[(2S)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione
C7 H11 F N4 O2
ZBKWVMMCABYTAU-BYPYZUCNSA-N
 Ligand Interaction
4WR
Query on 4WR

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Download CCD File 
B, D
1-[(2R)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione
C7 H11 F N4 O2
ZBKWVMMCABYTAU-SCSAIBSYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, C, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
F
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.208 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 91.280α = 90.00
b = 91.280β = 90.00
c = 137.227γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release