6FBA

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 2,3-naphthalenediol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Identification of a non-competitive inhibitor of Plasmodium falciparum aspartate transcarbamoylase.

Lunev, S.Bosch, S.S.Batista, F.A.Wang, C.Li, J.Linzke, M.Kruithof, P.Chamoun, G.Domling, A.S.S.Wrenger, C.Groves, M.R.

(2018) Biochem Biophys Res Commun 497: 835-842

  • DOI: https://doi.org/10.1016/j.bbrc.2018.02.112
  • Primary Citation of Related Structures:  
    6FBA

  • PubMed Abstract: 

    Aspartate transcarbamoylase catalyzes the second step of de-novo pyrimidine biosynthesis. As malarial parasites lack pyrimidine salvage machinery and rely on de-novo production for growth and proliferation, this pathway is a target for drug discovery. Previously, an apo crystal structure of aspartate transcarbamoylase from Plasmodium falciparum (PfATC) in its T-state has been reported. Here we present crystal structures of PfATC in the liganded R-state as well as in complex with the novel inhibitor, 2,3-napthalenediol, identified by high-throughput screening. Our data shows that 2,3-napthalediol binds in close proximity to the active site, implying an allosteric mechanism of inhibition. Furthermore, we report biophysical characterization of 2,3-napthalenediol. These data provide a promising starting point for structure based drug design targeting PfATC and malarial de-novo pyrimidine biosynthesis.


  • Organizational Affiliation

    Faculty of Science and Engineering, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands. Electronic address: m.r.groves@rug.nl.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate transcarbamoylase
A, B
349Plasmodium falciparumMutation(s): 0 
Gene Names: ATCase
EC: 2.1.3.2
UniProt
Find proteins for O15804 (Plasmodium falciparum)
Explore O15804 
Go to UniProtKB:  O15804
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15804
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate transcarbamoylase349Plasmodium falciparumMutation(s): 0 
Gene Names: ATCase
EC: 2.1.3.2
UniProt
Find proteins for O15804 (Plasmodium falciparum)
Explore O15804 
Go to UniProtKB:  O15804
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15804
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D48 (Subject of Investigation/LOI)
Query on D48

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
O [auth C]
naphthalene-2,3-diol
C10 H8 O2
JRNGUTKWMSBIBF-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
N [auth B],
Q [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
R [auth C]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
S [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
P [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
C
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
D48 Binding MOAD:  6FBA Kd: 1.99e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.757α = 90
b = 86.757β = 90
c = 138.151γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
DIMPLEmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references
  • Version 1.2: 2018-03-14
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description