2GUU

crystal structure of Plasmodium vivax orotidine 5-monophosphate decarboxylase with 6-aza-UMP bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of Plasmodium vivax orotidine 5-monophosphate decarboxylase with 6-aza-UMP bound

DONG, A., LEW, J., ZHAO, Y., Sundararajan, E., WASNEY, G., VEDADI, M., KOEIERADZKI, I., EDWARDS, A.M., ARROWSMITH, C.H., WEIGELT, J., SUNDSTROM, M., Pai, E.F., Kotra, L., BOCHKAREV, A., HUI, R., AMANI, M.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ODcase353Plasmodium vivaxMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UP6
Query on UP6
Download Ideal Coordinates CCD File 
B [auth A]6-AZA URIDINE 5'-MONOPHOSPHATE
C8 H12 N3 O9 P
LRVZOSYMNMNQFR-SHUUEZRQSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.731α = 90
b = 82.151β = 90
c = 59.739γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description