3ENZ

Arsenolytic structure of Plasmodium falciparum purine nucleoside phosphorylase with hypoxanthine, ribose and arsenate ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases.

Chaikuad, A.Brady, R.L.

(2009) BMC Struct Biol 9: 42-42

  • DOI: 10.1186/1472-6807-9-42
  • Primary Citation of Related Structures:  
    3EMV, 3ENZ

  • PubMed Abstract: 
  • Purine nucleoside phosphorylase (PNP) is central to purine salvage mechanisms in Plasmodium parasites, the causative agents of malaria. Most human malaria results from infection either by Plasmodium falciparum (Pf), the deadliest form of the parasite, or by the widespread Plasmodium vivax (Pv) ...

    Purine nucleoside phosphorylase (PNP) is central to purine salvage mechanisms in Plasmodium parasites, the causative agents of malaria. Most human malaria results from infection either by Plasmodium falciparum (Pf), the deadliest form of the parasite, or by the widespread Plasmodium vivax (Pv). Whereas the PNP enzyme from Pf has previously been studied in detail, despite the prevalence of Pv little is known about many of the key metabolic enzymes from this parasite, including PvPNP.


    Organizational Affiliation

    Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK. Apirat.Chaikuad@sgc.ox.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA, B, C, D, E, F253Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PFE0660cPF3D7_0513300
EC: 2.4.2.1
UniProt
Find proteins for Q8I3X4 (Plasmodium falciparum (isolate 3D7))
Explore Q8I3X4 
Go to UniProtKB:  Q8I3X4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ART
Query on ART

Download Ideal Coordinates CCD File 
I [auth A], JA [auth D], T [auth B], TA [auth E], XA [auth F], Z [auth C]ARSENATE
As O4
DJHGAFSJWGLOIV-UHFFFAOYSA-K
 Ligand Interaction
HPA
Query on HPA

Download Ideal Coordinates CCD File 
G [auth A], HA [auth D], R [auth B], RA [auth E], VA [auth F], X [auth C]HYPOXANTHINE
C5 H4 N4 O
FDGQSTZJBFJUBT-UHFFFAOYSA-N
 Ligand Interaction
R1X
Query on R1X

Download Ideal Coordinates CCD File 
H [auth A], IA [auth D], S [auth B], SA [auth E], WA [auth F], Y [auth C]1,4-anhydro-D-ribitol
C5 H10 O4
KZVAAIRBJJYZOW-LMVFSUKVSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
AA [auth C] , AB [auth F] , BA [auth C] , CA [auth C] , DA [auth C] , EA [auth C] , FA [auth C] , J [auth A] , 
AA [auth C],  AB [auth F],  BA [auth C],  CA [auth C],  DA [auth C],  EA [auth C],  FA [auth C],  J [auth A],  K [auth A],  KA [auth D],  L [auth A],  LA [auth D],  M [auth A],  MA [auth D],  N [auth A],  NA [auth D],  O [auth A],  OA [auth D],  P [auth A],  U [auth B],  UA [auth E],  V [auth B],  YA [auth F],  ZA [auth F]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
GA [auth C], PA [auth D], Q [auth A], QA [auth D], W [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.82α = 90
b = 177.82β = 90
c = 253.868γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations