7OOG

Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain in complex with NCL-00023823


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 ?
  • R-Value Free: 0.234 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structures of the Plasmodium falciparum heat-shock protein 70-x ATPase domain in complex with chemical fragments identify conserved and unique binding sites.

Mohamad, N.O'Donoghue, A.Kantsadi, A.L.Vakonakis, I.

(2021) Acta Crystallogr F Struct Biol Commun 77: 262-268

  • DOI: https://doi.org/10.1107/S2053230X21007378
  • Primary Citation of Related Structures:  
    7OOE, 7OOG, 7P31

  • PubMed Abstract: 

    Plasmodium falciparum invades erythrocytes and extensively modifies them in a manner that increases the virulence of this malaria parasite. A single heat-shock 70?kDa-type chaperone, PfHsp70-x, is among the parasite proteins exported to the host cell. PfHsp70-x assists in the formation of a key protein complex that underpins parasite virulence and supports parasite growth during febrile episodes. Previous work resolved the crystallographic structures of the PfHsp70-x ATPase and substrate-binding domains, and showed them to be highly similar to those of their human counterparts. Here, 233 chemical fragments were screened for binding to the PfHsp70-x ATPase domain, resulting in three crystallographic structures of this domain in complex with ligands. Two binding sites were identified, with most ligands binding proximal to the ATPase nucleotide-binding pocket. Although amino acids participating in direct ligand interactions are conserved between the parasite and human erythrocytic chaperones, one nonconserved residue is also present near the ligand. This work suggests that PfHsp70-x features binding sites that may be exploitable by small-molecule ligands towards the specific inhibition of the parasite chaperone.


  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein 70
A, B
393Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0831700
UniProt
Find proteins for K7NTP5 (Plasmodium falciparum (isolate 3D7))
Explore K7NTP5 
Go to UniProtKB:  K7NTP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7NTP5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AN2
Query on AN2

Download Ideal Coordinates CCD File 
E [auth A],
S [auth B]
AMP PHOSPHORAMIDATE
C10 H16 N6 O9 P2
FQMDCEJHLOLKLI-KQYNXXCUSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
HEW (Subject of Investigation/LOI)
Query on HEW

Download Ideal Coordinates CCD File 
M [auth A],
X [auth B]
4-bromanylpyridin-2-amine
C5 H5 Br N2
BAQKUNMKVAPWGU-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
N [auth A],
Y [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
C [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
R [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
O [auth A],
P [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
Q [auth A],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 ?
  • R-Value Free: 0.234 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( ? )Angle ( ? )
a = 79.997¦Á = 90
b = 101.027¦Â = 90
c = 103.184¦Ã = 90
Software Package:
Software NamePurpose
BUSTERrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R021759/1
H2020 Marie Curie Actions of the European CommissionEuropean Union752069

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-09-25
    Changes: Database references
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