3OZF | pdb_00003ozf

Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with hypoxanthine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.237 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3OZF

This is version 1.3 of the entry. See complete history

Literature

Acyclic Immucillin Phosphonates: Second-Generation Inhibitors of Plasmodium falciparum Hypoxanthine- Guanine-Xanthine Phosphoribosyltransferase.

Hazleton, K.Z.Ho, M.C.Cassera, M.B.Clinch, K.Crump, D.R.Rosario, I.Merino, E.F.Almo, S.C.Tyler, P.C.Schramm, V.L.

(2012) Chem Biol 19: 721-730

  • DOI: https://doi.org/10.1016/j.chembiol.2012.04.012
  • Primary Citation Related Structures: 
    3OZF, 3OZG

  • PubMed Abstract: 

    Plasmodium falciparum, the primary cause of deaths from malaria, is a purine auxotroph and relies on hypoxanthine salvage from the host purine pool. Purine starvation as an antimalarial target has been validated by inhibition of purine nucleoside phosphorylase. Hypoxanthine depletion kills Plasmodium falciparum in cell culture and in Aotus monkey infections. Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from P. falciparum is required for hypoxanthine salvage by forming inosine 5'-monophosphate, a branchpoint for all purine nucleotide synthesis in the parasite. Here, we present a class of HGXPRT inhibitors, the acyclic immucillin phosphonates (AIPs), and cell permeable AIP prodrugs. The AIPs are simple, potent, selective, and biologically stable inhibitors. The AIP prodrugs block proliferation of cultured parasites by inhibiting the incorporation of hypoxanthine into the parasite nucleotide pool and validates HGXPRT as a target in malaria.


  • Organizational Affiliation
    • Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA.

Macromolecule Content 

  • Total Structure Weight: 115.42 kDa 
  • Atom Count: 7,955 
  • Modeled Residue Count: 923 
  • Deposited Residue Count: 1,000 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypoxanthine-guanine-xanthine phosphoribosyltransferase
A, B, C, D
250Plasmodium falciparum FCR-3/GambiaMutation(s): 0 
Gene Names: LACZ
EC: 2.4.2 (PDB Primary Data), 2.4.2.22 (UniProt), 2.4.2.8 (UniProt)
UniProt
Find proteins for P20035 (Plasmodium falciparum (isolate FCR-3 / Gambia))
Explore P20035 
Go to UniProtKB:  P20035
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20035
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POP

Query on POP



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
N [auth C],
V [auth D]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
HPA

Query on HPA



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
M [auth C],
U [auth D]
HYPOXANTHINE
C5 H4 N4 O
FDGQSTZJBFJUBT-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
O [auth C],
R [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A]
L [auth B]
P [auth C]
Q [auth C]
S [auth D]
H [auth A],
L [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.035α = 90
b = 88.907β = 117.06
c = 80.371γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2012-07-11
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations