7P31

Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain in complex with NCL-00023818

• PDB DOI: https://doi.org/10.2210/pdb7P31/pdb

• Classification: CHAPERONE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-06 Released: 2021-07-14 
• Deposition Author(s): Mohamad, N., O'Donoghue, A., Kantsadi, A.L., Vakonakis, I.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.235 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7ooh

Literature

Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain in complex with small molecule ligands

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 88.03 kDa 
• Atom Count: 6,102 
• Modelled Residue Count: 762 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein 70	A, B	393	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF3D7_0831700
UniProt
Find proteins for K7NTP5 (Plasmodium falciparum (isolate 3D7)) Explore K7NTP5  Go to UniProtKB:  K7NTP5

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AN2	D [auth A], M [auth B]	AMP PHOSPHORAMIDATE C10 H16 N6 O9 P2 FQMDCEJHLOLKLI-KQYNXXCUSA-N
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PYZ (Subject of Investigation/LOI)	F [auth A], O [auth B]	4-IODOPYRAZOLE C3 H3 I N2 LLNQWPTUJJYTTE-UHFFFAOYSA-N
IOD	R [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
PO4	I [auth A], Q [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], G [auth A], H [auth A], L [auth B], N [auth B], P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.235 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.979	α = 90
b = 102.575	β = 90
c = 103.829	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Mohamad, N., O'Donoghue, A., Kantsadi, A.L., Vakonakis, I.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R021759/1
H2020 Marie Curie Actions of the European Commission	European Union	752069

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description